Can't get rid of "file to commit"

For any strange reason whenever I do commit project a certain class shows up as to be committed, even though it contains no changes at all: Tools.java
I tried anything I could think of, still whenever I issue commit the file is back:
Make a change, then revert.
Did a cleanup on the directory in Tortoise.
Even deleted the whole directory containing the file and did an update to get a fresh copy.

Doing a "Compare with the last repository version" always says "Contents are identical".

It might be a problem, that I have two modules where one module's content root is inside the content root of the other module (don't blame me - it's a 3rd party product, where we simply do some customizations).

Known bug? Anything more I can do to help diagnose the problem?

As a workaround I moved the file to another changelist.

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