Andrew,
I looked at your debug log and unfortunately did not see any clues there. Also, I compared the PHD1 and PHD2 code and can't see anything obvious for why subframes would work in PHD1 and not in PHD2 -- the code for the Atik 16 camera is very nearly identical.
The next thing to do would be to put together a special build that adds more detailed logging to see why you are not getting subframes. I will contact you off-list to see if you want to pursue this.
Regarding your question about restarting PHD: no, that should not make any difference. Going forward, it may be more convenient for you to create two equipment profiles: one for the Atik and one for the SSAG. Each profile has its own settings--things like pixel size, dark frames, calibration data, etc. When you switch cameras, you would just select the corresponding equipment profile, connect your equipment, and go.
Andy