Werner
pfm Member
It surprised me that 44.1k and 48k efforts to reproduce a square wave in Audacity sounded so different, and could only be described as a dramatic fail.
Once more:
1) there are issues with synthetically generating such waveforms in a frequency-limited sampled space.
2) there are known issues with Audacity.
3) it remains to be seen how your PC's OS and sound card handle the resultant files with differing sample rates. Uninteded SRC is likely to happen on at least one file.
Resolve all of these, and then come back if they still sound different.