Based on the smallish screenshots, I believe I've experienced similar symptoms in the past with two different recorders. One was a screwy power source connector (forget which recorder). The other, with an MTI, was a bad coax cable. I know you say in your OP all the cables are good. Are you sure, i.e. have you tested the gear/cables post-problem to confirm?
Edit to add: Just listened to the drum sample. It's quite obvious where the channels swap. But I don't hear the click/pop I heard in the symptoms I experienced with my issues. Hmmm.
Edit again: Do you have a soundcard with digital-in that you can use to take the MTI out of the recording chain? Another digital cable to swap out? Another ADC with which to feed the MTI? At this point, I think you need to start isolating the problem by swapping out components for known-good (or at least different) gear.