Scrub trimmer moves audio out of sync.
This is a known issue and should be fixed in a future release.
To get back in sync, after the undo and the sync marks appear, go to spot mode w/ the grabber tool. Click on the region and enter in the start time as the sync point time. Click OK.

To reproduce: Record audio on a track. In slip mode, scrub trim it to the right. Control drag that new region from the list to the track below. Scrub trim both tracks together to the left, by placing the scrub trim tool over both tracks. The selection goes left, but the waveform does not. All audio has moved right the amount you scrub trimmed left. The regions tail is now cut off. Selecting undo deslects the non audio portion of the selection of the region and creates a sync point that is equal in length to the non audio portion that was unselected, but does not move the region back to its' original