Randy,
The first time you run PHD2 you definitely want to get through calibration manually. After that, you can re-use that calibration data (assuming you mark it to save/restore calibration). SGP doesn't understand what is happening while PHD2 does a calibration and it can lead to issues if you're relying on it. I always do a manual calibration when I change things.
You need to make sure you save your profiles after you edit them. I use the option under 'File' to save the current profile.
Hope that helps,
Chris