›_ Claude Code Issues
Claude Code Issues / #56858

[BUG] Claude Desktop 1.6259.1.0 — MCP servers show "running" in Settings but tools never reach servers from chat

Resolved 💬 1 comment Opened May 7, 2026 by Dcrts Closed Jun 5, 2026

Preflight Checklist

  • [x] I have searched existing issues and this hasn't been reported yet
  • [x] This is a single bug report (please file separate reports for different bugs)
  • [x] I am using the latest version of Claude Code

What's Wrong?

Title

[BUG] Claude Desktop 1.6259.1.0 — MCP servers show "running" in Settings but tools never reach servers from chat

Preflight Checklist

  • [x] Searched existing issues
  • [x] Single bug report
  • [x] Using latest Claude Desktop version (1.6259.1.0)

What's wrong

After updating Claude Desktop to version 1.6259.1.0 on Windows (MSIX install),
local MCP servers (filesystem, postgres) start successfully and show "running"
status in Settings → Developer → Local MCP servers, but tool calls from chat
never reach the servers.

This is a regression — the same configuration worked correctly on previous
Claude Desktop version (used daily since 2026-05-02 for AI Wine project).

Symptoms

  • MCP servers show green "running" badge in Settings
  • Server logs show successful initialization handshake
  • No tools/call messages appear in server logs after handshake completes
  • In chat sessions, when asking Claude to use filesystem or postgres tools,

Claude reports MCP tools are "not available" or hangs indefinitely

  • Manual server invocation from PowerShell works perfectly (servers respond

to direct queries and return correct data)

Environment

  • Windows 11
  • Claude Desktop 1.6259.1.0 (MSIX install from official anthropic.com)
  • Config path: %LOCALAPPDATA%\Packages\Claude_pzs8sxrjxfjjc\LocalCache\Roaming\Claude\claude_desktop_config.json
  • Hardware: 128 GB RAM, RTX 5090

Reproduction steps

  1. Configure local MCP server in claude_desktop_config.json:
"postgres": {
  "command": "C:\\Users\\<user>\\.local\\bin\\postgres-mcp.exe",
  "args": ["--access-mode=restricted"],
  "env": {
    "DATABASE_URI": "postgresql://user:pass@localhost:5432/db"
  }
}
  1. Restart Claude Desktop completely (Get-Process claude | Stop-Process -Force)
  2. Open Settings → Developer → Local MCP servers — confirm postgres shows

"running"

  1. Open new chat session in any project
  2. Ask Claude to query the database via MCP
  3. Observe: Claude reports MCP tools unavailable, no SQL query reaches server

Expected behavior

When MCP server shows "running" in Settings, chat sessions should have access
to tools provided by that server.

Additional context

This appears related to issue #22299 (CCD v2.1.22 regression on Windows) but
manifesting in the unified Chat/Code/Cowork desktop architecture introduced
in version 1.6259.x.

The Code section (Claude Code integrated into desktop) maintains filesystem
access through different mechanism (bash tools), but Chat section completely
loses MCP integration despite servers being properly running.

This breaks workflows that depend on filesystem and database access from
Chat for projects requiring document analysis, schema inspection, and live
data validation.

Severity

High — blocks core workflows that depend on MCP integration in Chat sessions.
No workaround possible from user side (servers are healthy, configuration
is correct, the routing layer in Claude Desktop is broken).

What Should Happen?

Title

[BUG] Claude Desktop 1.6259.1.0 — MCP servers show "running" in Settings but tools never reach servers from chat

Preflight Checklist

  • [x] Searched existing issues
  • [x] Single bug report
  • [x] Using latest Claude Desktop version (1.6259.1.0)

What's wrong

After updating Claude Desktop to version 1.6259.1.0 on Windows (MSIX install),
local MCP servers (filesystem, postgres) start successfully and show "running"
status in Settings → Developer → Local MCP servers, but tool calls from chat
never reach the servers.

This is a regression — the same configuration worked correctly on previous
Claude Desktop version (used daily since 2026-05-02 for AI Wine project).

Symptoms

  • MCP servers show green "running" badge in Settings
  • Server logs show successful initialization handshake
  • No tools/call messages appear in server logs after handshake completes
  • In chat sessions, when asking Claude to use filesystem or postgres tools,

Claude reports MCP tools are "not available" or hangs indefinitely

  • Manual server invocation from PowerShell works perfectly (servers respond

to direct queries and return correct data)

Environment

  • Windows 11
  • Claude Desktop 1.6259.1.0 (MSIX install from official anthropic.com)
  • Config path: %LOCALAPPDATA%\Packages\Claude_pzs8sxrjxfjjc\LocalCache\Roaming\Claude\claude_desktop_config.json
  • Hardware: 128 GB RAM, RTX 5090

Reproduction steps

  1. Configure local MCP server in claude_desktop_config.json:
"postgres": {
  "command": "C:\\Users\\<user>\\.local\\bin\\postgres-mcp.exe",
  "args": ["--access-mode=restricted"],
  "env": {
    "DATABASE_URI": "postgresql://user:pass@localhost:5432/db"
  }
}
  1. Restart Claude Desktop completely (Get-Process claude | Stop-Process -Force)
  2. Open Settings → Developer → Local MCP servers — confirm postgres shows

"running"

  1. Open new chat session in any project
  2. Ask Claude to query the database via MCP
  3. Observe: Claude reports MCP tools unavailable, no SQL query reaches server

Expected behavior

When MCP server shows "running" in Settings, chat sessions should have access
to tools provided by that server.

Additional context

This appears related to issue #22299 (CCD v2.1.22 regression on Windows) but
manifesting in the unified Chat/Code/Cowork desktop architecture introduced
in version 1.6259.x.

The Code section (Claude Code integrated into desktop) maintains filesystem
access through different mechanism (bash tools), but Chat section completely
loses MCP integration despite servers being properly running.

This breaks workflows that depend on filesystem and database access from
Chat for projects requiring document analysis, schema inspection, and live
data validation.

Severity

High — blocks core workflows that depend on MCP integration in Chat sessions.
No workaround possible from user side (servers are healthy, configuration
is correct, the routing layer in Claude Desktop is broken).

Error Messages/Logs

Steps to Reproduce

Title

[BUG] Claude Desktop 1.6259.1.0 — MCP servers show "running" in Settings but tools never reach servers from chat

Preflight Checklist

  • [x] Searched existing issues
  • [x] Single bug report
  • [x] Using latest Claude Desktop version (1.6259.1.0)

What's wrong

After updating Claude Desktop to version 1.6259.1.0 on Windows (MSIX install),
local MCP servers (filesystem, postgres) start successfully and show "running"
status in Settings → Developer → Local MCP servers, but tool calls from chat
never reach the servers.

This is a regression — the same configuration worked correctly on previous
Claude Desktop version (used daily since 2026-05-02 for AI Wine project).

Symptoms

  • MCP servers show green "running" badge in Settings
  • Server logs show successful initialization handshake
  • No tools/call messages appear in server logs after handshake completes
  • In chat sessions, when asking Claude to use filesystem or postgres tools,

Claude reports MCP tools are "not available" or hangs indefinitely

  • Manual server invocation from PowerShell works perfectly (servers respond

to direct queries and return correct data)

Environment

  • Windows 11
  • Claude Desktop 1.6259.1.0 (MSIX install from official anthropic.com)
  • Config path: %LOCALAPPDATA%\Packages\Claude_pzs8sxrjxfjjc\LocalCache\Roaming\Claude\claude_desktop_config.json
  • Hardware: 128 GB RAM, RTX 5090

Reproduction steps

  1. Configure local MCP server in claude_desktop_config.json:
"postgres": {
  "command": "C:\\Users\\<user>\\.local\\bin\\postgres-mcp.exe",
  "args": ["--access-mode=restricted"],
  "env": {
    "DATABASE_URI": "postgresql://user:pass@localhost:5432/db"
  }
}
  1. Restart Claude Desktop completely (Get-Process claude | Stop-Process -Force)
  2. Open Settings → Developer → Local MCP servers — confirm postgres shows

"running"

  1. Open new chat session in any project
  2. Ask Claude to query the database via MCP
  3. Observe: Claude reports MCP tools unavailable, no SQL query reaches server

Expected behavior

When MCP server shows "running" in Settings, chat sessions should have access
to tools provided by that server.

Additional context

This appears related to issue #22299 (CCD v2.1.22 regression on Windows) but
manifesting in the unified Chat/Code/Cowork desktop architecture introduced
in version 1.6259.x.

The Code section (Claude Code integrated into desktop) maintains filesystem
access through different mechanism (bash tools), but Chat section completely
loses MCP integration despite servers being properly running.

This breaks workflows that depend on filesystem and database access from
Chat for projects requiring document analysis, schema inspection, and live
data validation.

Severity

High — blocks core workflows that depend on MCP integration in Chat sessions.
No workaround possible from user side (servers are healthy, configuration
is correct, the routing layer in Claude Desktop is broken).

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

Claude 1.6259.1.0

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

_No response_

View original on GitHub ↗

This issue has 1 comment on GitHub. Read the full discussion on GitHub ↗