Your 68040.library version seems ok, but it doesn't rule out that it's not corrupted.
Corruption of files could be caused by incorrect mask setting if using a CF card as a hard drive on the internal IDE (A1200, A600, A4000).
Are you using SFS? Are you using your CF now or a real hard drive? I believe SFS has different versions depending on which CPU your Amiga has...so it's worth checking you're using the correct version.
Try replacing the 68040.library with the one from your OS Install disk (I think it resides on that disk anyway).