Hey, thanks for the detailed report with all the diagnostic data.
This is a known bug in the Glass layout. The Changes panel sometimes gets out of sync with the real git state and shows No Local Changes or Initialize Repository even when there are changes. A few users have hit variations of this issue:
The team is aware of it, and your report helps with prioritization.
Let me know if you notice any more details about the pattern of when this happens, like after specific agent actions.