1. Carefully made a 9 bar selection, snapped to the grid, so that I could cut and paste some audio clips that were aligned correctly but not starting on measure boundaries. eg. Audio clip starts at 8:03:050, so I selected started from 8:01:000. Pasted it elsewhere, and saw that Sonar 'helpfully' changes the size of the selection to starts at the start of the earliest clip, meaning it pastes in at an unexpected position that is no longer aligned relative to measures. Thanks! I had to artificially extend the clips to measure boundaries, cut/paste them, then trim them again.
2. Stretched audio (via ctrl-slip-edit) occasionally plays back with major glitches - i.e. peaks of +9.0dB, even +99dB once! Bounce-to-clip solves the problem, but something was obviously broken.
3. The first time I hit Play after switching from one open project to another, I often get a high pitched squeal instead of my audio. Occasionally I get no audio at all. Stopping and restarting transport fixes that.
4. Snap-offsets getting messed up when I do anything involving time-stretching clips where the underlying audio appears in more than one clip... that wastes my time and requires a bounce, too.
All these problems have workarounds, but it's tiring to run into these issues when I'm trying to be creative!