Well, it seems that the source WAV is OK, the FLACs are variously bad on each successive FLACing. So, hardware or software? The machine is working well otherwise, so I would concentrate on the software. foobar2000 will do a nice job of running FLAC. So will the FLAC "front end" which is just a menuing program to run the flac.exe file. CD Wave Editor will also run FLAC compression.
So, I would FLAC one file, the same one, with CD Wave Editor, foobar2000 and FLAC front end. See which one is failing. If it shows up with this test we are pretty sure we will have found the offending software package.
What release of FLAC are you using??? 1.1.4 is current.
Cheers
