Do you happen to have a user configured ALSA configuration (in /home/pi/.asoundrc), that was used to do some software equalization? I know a couple of our customers experimented with that…
This would override AmpliPi’s global ALSA configuration (set in /etc/asound.conf) and has the potential to cause lots of weird issues such as this.
Either way my instincts are this is an ALSA configuration/hardware issue. To check could you send us the output of the following commands (over an ssh session):
aplay -L
aplay -l
These will tell us what the sound hardware looks like and how it is configured.