Sampled from right channel output (left has same issue). The bottom half of the waveform is clipped in this way, starting with Paula pins 33 and 34. Does this mean Paula is bad, or could it be something else?
I should have updated the description to say I've fixed the problem. It ended up being that my -12v rail was missing, so the op amp couldn't go negative. I pulled the motherboard out of an old Magicbox Alphagen character generator (which is based on a slightly modified A1200), and that system never had a -12v rail at all, since they never used the audio outputs for anything. So, when I was building a new supply, I simply overlooked the requirement. Thanks for the suggestions though!
If the reference voltage is completely off, you need to check capacitor C305 and C306. Also check R303 and R304. However, it's more likely to be the caps. If AVref checks ok, there might instead be a problem with the supply voltage for the OP-amps. Check R301, R302, C301, C302, C303 and C304 if you are not getting around +12V and -12V at the supply rails for the OP-amp.
The audio circuit pretty much works the same on every Amiga model. I made a video where I documented the repair of an Amiga 4000 that had an audio problem. You can check it out if you want, maybe you can find some more info there.
You shouldn't get any output at all when probing the output pins on Paula, because when doing so you are also probing the inverting inputs of the op-amps that are set up as inverting amplifiers/integrators. These inputs will always be at AVref. You can probe the outputs on the op-amp to get a reading on the scope. It looks on the scope like your audio is clipping. Check the reference voltage at the op-amp. It should be around 2.5V.