David,
I agree with Bret: it would help to know your camera and how you are using it--guidescope? OAG? if OAG, what scope?
One other thing to check would be the gain setting on the camera tab in the brain. Is it set to the the same value in PHD1 and PHD2?
It would be great if you could do a controlled experiment, with the scope tracking and pointing to one position in the sky. Start PHD1, connect camera, loop, stop, save image (File => Save Image). Then repeat immediately with PHD2 (same exposure duration and gain setting). Then you can post the two FITS images for comparison. Also, if you do this, please post the debug logs (PHD2_DebugLog_<date-time>.txt in the PHD2 folder in your Documents folder for PHD2; and the PHD debug log directly in the Documents folder.) Also, when you do this experiment you could post screenshots showing us what you see and where the gamma slider is is phd1 and phd2.
Andy