As a farm admin i've all rights, creating an new project resulted into me being:
- project manager in TFS
- full control in Sharepoint
- content manager in report builder
I used the TFSAdmin tool and clicked off the checkbox 'content manager' under report server and then i clicked it on again.
In fact i didn't change anything this time, but the commit changes is tracking every action (even if it's a wrong one)
In my opinion the "commit changes" should only commit the differences between the original state and the final state
Or even better (but that is another Issue?) don't allow tfsadmin to remove your own permissions..