Yeah no I'm afraid that's not it either David. I thought so too for a second but the guitar amp signal transient is never behind the big transient of a guitar DI signal. Also when I moved the faulty regions to match the Q-ref the transient markers went to single markers.
In other words, I have no idea what causes this issue or how to prevent it. But to solve it you can move the region to match up the transients, then press opt+cmd+Q followed by Q for quantize. Sometimes it only works if you press these shortcuts twice. By "works" I mean the double transient markers are gone and both tracks sync up. So problem solved, sort of.