The PHD2 User Manual describes how to determine whether or not you need to check the "reverse dec output after meridian flip" option. Here's the link: http://openphdguiding.org/manual/?section=Advanced_settings.htm. Scroll down to Shared Guiding Parameters, Reverse Dec output after meridian flip.
Or, you can post your PHD2 Guide Log and we can answer your question by looking at that ("all over the place" is not specific enough information.)
Andy