It is always helpful for us to know the exact presets involved. Many times people think a particular problem occurs all the time, whereas in reality it only happens in certain cirumstances, i.e. with certain presets.
Eventide recommends that you perform a "Clear Setup" operation after every upgrade – this returns the unit to factory defaults and gets it into a known state. You can do it by holding down the SETUP key at powerup – it won't erase user presets. You will then have to redo any non-default settings.
