I decompressed the FLAC and did an MD5sum on the resulting WAV. It mached the original WAV perfectly. I repeated this several times on different FLACs whenever the distortion appeared. Always the correct MD5sum.
I think I figured it out. The MD5 match does not say that the compared files are necessarily also a bit to bit match. It only says they are bit to bit match with very high probabilty. Nevermind how small the chance is for two files being different while having the same MD5 - it obviously did happen in your case - and even worse: not only once, byt multiple times on every single flac file examined, which leads me to an inevitable, almost crazy sounding (still I couldn't believe it myself at first) conclusion, that the FLAC encoder does use lossy compresion and to cover it up, it than changes some bits on the output so, that the resulting files give exactly same MD5's as the original ones and thus gaining imunity against MD5 attacks. I am really, really disapointed from FLAC after reading this thread, it is so obvious that this so called FLAC is nothing more than only cheap hype.
Yeah... you may say, that this is only a conspiracy theory and you can laugh at me, perhaps disagree with me. But you know waht ? There isn't much more you can do about it, coz it's definitely TRUE.
If I didn't mention it yet: big thanks for this thread, which really helped me to open my eyes and to get rid of some prevailing myths about FLAC (e.g. FLAC being lossless) and I am eager to see some more quality stuff like "FLAC vs. CDA", WAV vs. CDA" and if that's not enough, than I am pretty shure that crunchy delicacy "Wav vs. Wav" should blow mind of almost every head-fier.