Hey, thanks for the report.
This is a known UX issue and the team is already tracking it. The problem is that Cloud Agents don’t work with Legacy Privacy Mode, but the UI doesn’t show a clear error message. Because of that, the branch selector just becomes disabled with no explanation.
Your fix is correct: Cursor Settings > General > Privacy Mode (turn off “Legacy”).
Other users have hit the same issue: GitHub Agent "Select Branch" Dropdown Disabled for Org Repo
The team is working on improving the UX for this case. They should add a clear error message instead of silently disabling the feature.