Hey, thanks for the report. This is a known issue, and the team is working on a fix.
Temporary workaround, it helps most users:
- Fully close Cursor
- Run the community script to reset the stuck flags in the database: MCP Allowlist doesn't work, also can't be edited - #19 by helloworld2
- Restart Cursor
After that, auto-run should work correctly with MCP tools. A few users confirmed this fixes the issue.
Let me know if the workaround helped.