Simplified and started from a clean slate, without much of the hidden existing space data that was hanging around in the old one. One issue I found is that saving the startup file from Blender 2.5 also saves the window size and location. This means the version I just saved would open up strangely on other screen sizes/setups. I added code to reset this to default when loading it up from the version compiled into the Blender binary, but perhaps Ton/ Brecht might want to check the diff.