Lets reiterate whats been said up thread it's not the file format itself but the on-the-fly transcoding that seems to bring about the apparent audible difference some peopple detect. Personally I've not noticed it and IVe done the Foobar ABX thing. What mechanism is at play here is anybody's guess.

On the file type itself, If you take a Wav file, create a duplicate, encode the duplicate, manually decode the Flac back to Wav and compare the duplicate to the original you will not find a difference. Perform a binary compare between the two and they will be identical.