I'm very sorry to hear that. Did the BoxCryptor program crash or did you even experience BSODs?
Data corruption caused by BoxCryptor would be absolutely unacceptable. Ensuring that data is written correctly is extremely important to us and the encryption part of BoxCryptor is tested extremely well. (Until now) we're not aware of a single case of a wrong data write caused by BoxCryptor.
The issue could be caused by other software components involved, e.g. anti-virus software, and a quick search in the FileMaker knowledge base for "corrupt" brought up several pages with information that even FileMaker itself could cause this. I'm not trying to blame others and I'm taking this extremely serious, but please keep this in mind.
Can you reproduce the issue with FileMaker or did it just happen accidentally? If you have any further information on this issue (FileMaker version, what kind of database did you save, etc.), it could help us.