Darth Mallwalker said:

When you made those recordings, did you press Record button before pressing Play?

no, there was enough time before the audio started. but usually i would press record before pressing play.

anyway... i tried to use the -s cmd with synced test-files and i get another weird result

/bitperfect_test/shntool cmp /bitperfect_test/ww1_mixdown.wav /bitperfect_test/ww2_mixdown.wav
Comparing [/bitperfect_test/ww1_mixdown.wav] (0:14.21) and [/bitperfect_test/ww2_mixdown.wav] (0:14.21) : 21% ERROR
shntool [cmp]: error: WAVE data differs at byte offset: 1

when i use the same files without the -s cmd, then i get this

/bitperfect_test/shntool cmp -s /bitperfect_test/ww1_mixdown.wav /bitperfect_test/ww2_mixdown.wav
Scanning [/bitperfect_test/ww1_mixdown.wav] and [/bitperfect_test/ww2_mixdown.wav] : 0% ERROR
shntool [cmp]: error: these files do not share identical data within the first 529200 bytes.