[BUG] Opus 4.1 model is not using MCP servers

Environment

• Platform (select one):
• [x] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 1.0.94
• Operating System: Windows 10
• Terminal: cmd

Bug Description

For some reason Claude Code is not using MCP tools when using Opus 4.1 Model. When I switch to Sonnet 4 it happily uses e.g. context7

Steps to Reproduce

1. Configure MCP servers in .mcp.json
2. Enable MCP servers in claude settings.json
3. Start claude and check mcp servers are connected
4. Perform code analysis or refactoring with Opus 4.1 Model vs Sonnet 4 Model.

Expected Behavior

That claude-code uses the MCP servers to lookup documentation/references and better navigate through the code and does not only rely on fuzzy regex searches.

Actual Behavior

Claude-code never invokes any MCP client.

Additional Context

.claude/settings.local.json

{
  "permissions": {
    "allow": [
      "Bash(awk:*)",
      "Bash(cat:*)",
      "Bash(chmod:*)",
      "Bash(cp:*)",
      "Bash(curl:*)",
      "Bash(diff:*)",
      "Bash(find:*)",
      "Bash(grep:*)",
      "Bash(ls:*)",
      "Bash(mkdir:*)",
      "Bash(mv:*)",
      "Bash(sed:*)",
      "Bash(tree:*)",
      "Bash(touch:*)",
      "mcp__context7",
      "mcp__dart-mcp",
      "mcp__git-mcp",
      "mcp__dart-lsp",
      "mcp__serena",
      "mcp__zen",
      "WebSearch"
    ],
    "deny": [],
    "additionalDirectories": [ ]
  },
  "enableAllProjectMcpServers": true,
  "enabledMcpjsonServers": [
    "context7",
    "dart-mcp",
    "git-mcp",
    "serena",
    "zen"
  ],
  "disabledMcpjsonServers": []
}

.mcp.json

{
   "mcpServers": {
      "dart-mcp": {
         "command": "C:\\scoop\\apps\\flutter\\current\\bin\\cache\\dart-sdk\\bin\\dart.exe",
         "args": [
            "mcp-server"
         ],
         "env": {}
      },
      "context7": {
         "command": "sh",
         "args": [
            "npx",
            "-y",
            "@upstash/context7-mcp"
         ]
      },
      "git-mcp": {
         "type": "sse",
         "url": "https://gitmcp.io/docs"
      },
      "serena": {
         "command": "uvx",
         "args": [
            "--from",
            "git+https://github.com/oraios/serena",
            "serena-mcp-server",
            "--context",
            "ide-assistant",
            "--enable-web-dashboard",
            "false",
            "--enable-gui-log-window",
            "false"
         ]
      },
      "zen": {
         "command": "uvx",
         "args": [
            "--from",
            "git+https://github.com/BeehiveInnovations/zen-mcp-server",
            "zen-mcp-server"
         ]
      }
   }
}