Rory Primrose | Using WinMerge with TFS:

Note: You need to click on the Save button on the tool bar within WinMerge merge to commit a merge before exiting the screen

I can't tell if this should fix things or not, but hitting Ctrl-S isn't working for me right now.  I go back into git after resolving the conflict with WinMerge and the conflict markers are still there.