OK, the pokemon don't seem to be warped but if I enter the summary screen it resets the game. Am I best scrapping my hack and just using this from a fresh rom?
Not at all. This was designed to work with progressing hacks. Try changing the location for the engine. The freezing on summary screen sounds to me like ability name/description names issue. Try erasing them for a while to insert a file in the 'repoints' file and see if it still freezes.