^Yeah, that's weird.

Maybe it's time for sanity checks.
Let's begin with a raw recording, and no leading silence.
Press Play, wait until the music starts before pressing Record.
I'll call it Take3.wav

Should match itself (we hope!)
shntool cmp Take3.wav Take3.wav

Next we'll test if "-s" is working correctly.

echo 0:02 | shntool split Take3.wav
That should produce two output files:
split-track01.wav (should be exactly 2 seconds long, or 88.200 samples)
split-track02.wav (the rest of it)

shntool cmp Take3.wav split-track01.wav
shntool cmp -s Take3.wav split-track02.wav
shntool cmp -s split-track02.wav Take3.wav

Are the results as expected?