[BUG] "Allow bypass permissions mode" setting enabled but sessions always start in Accept Edits mode

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?

The "Allow bypass permissions mode" toggle in Settings > Claude Code is turned ON, but every new session starts in "Accept Edits" mode. A yellow warning appears at the top saying: "Bypass Permissions mode isn't enabled. The session started in Accept Edits — enable Bypass Permissions in Settings to use it."

The setting visually persists (doesn't flip back to off), but it has no effect on session startup.

What Should Happen?

When "Allow bypass permissions mode" is enabled in Settings, all new sessions should automatically start in Bypass Permissions mode without requiring any additional action from the user.

Error Messages/Logs

Steps to Reproduce

1. Open Claude Code desktop app (Windows)
2. Go to Settings > Claude Code
3. Enable "Allow bypass permissions mode" toggle (turns blue)
4. Close Settings
5. Start a new session (or use existing session)
6. Yellow warning appears: "Bypass Permissions mode isn't enabled. The session started in Accept Edits"

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

1.9255.2

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

_No response_