Hey all. Thanks for the replies!
Firmware version is 2.10
I've tried both a strat with EMG's and a tele with dual humbuckers. In both cases I've tried with PAD on/off, via headphones direct out of the POD and via headphones and monitors out of the MOTO (XLR out from POD to MOTU). I've tried with the master on the POD hot, with it low. The only thing that works is to back off the volume on the guitar(s) and/or to back off the drive on the amp models ... but it doesn't stop that unwanted distortion until there's pretty much no wanted distortion (e.g. 0:26ish on the sample.)
bjnette: if it's clipping, it's internal, I hear it no matter what I output to (headphones out from the pod, XLR out to MOTU, etc)
evilmikehoo: I assumed at first that it was the signal being too hot from my strat with EMGs as well; however, the only way I can get rid of it is to cool the signal (before the POD or via drive) to the point that there's pretty much no distortion left.
martindorr: thanks, I'll see if I can figure out where my input levels are at specifically, but again, I've tried cooling them down quite a bit and can't seem to eliminate the clipping without simultaneously eliminating the actual drive/distortion wanted in the tone.
stumblinman: I seem to have the most up-to-date firmware, and yes, with the guitar level low but the amp drive/channel volume up, the clipping sound is still there.
Thanks all! I've also submitted a tech support ticket.