I've had a similar problem when checking in source code to a project that was still open in its IDE. After exiting the IDE, the check in completed without a hitch. My conjecture is that the IDE (Microchip's MPLAB in this case) was keeping some of its workspace files in flux as long as the project was open.

I haven't attempted to diagnose this in more detail, since the simple rule of closing the project before doing the final check in and wrapping up a delivery bundle fit well enough into my workflow.