Talking about a roller coaster... I uninstalled papywizard, deleted the folder under the user/roaming directory and reinstalled. Now its working! I had to spin the pitch forwards to where I just let it run to get it back to 0 or else it always was -3780. Now when the unit starts up its at 0 which is where it should be.
I don't think it had anything to do with your Papywizard installation, but whatver it was you seem to have resolved it.
I have the feeling that you may not yet have fully grasped the idea of setting the Reference (zero pitch/zero yaw) position. You can set/reset this at any time. Use the arrow keys to move the head to the desired Reference position and then use the Hardware/Set Reference command to assign the zero/zero co-ordinates to this position- see screenshot 1. This Reference position is only maintained until you power off the Merlin mount, it's not 'smart' enough to remember the Reference position over a power-cycle, so you should re-establish the Reference position each time you power up the Merlin mount.
One observation however sometime in the mosaic the shooting menu the area is filled pink and won't shoot. I think that happens when the batteries are low, however what other conditions cause that?
Can we see a screenshot showing the effect you describe? I've always used a mains adapeter or an external battery pack with my Merlin. Do you have the Panogear package with the Lithium Ion battery enhancement or a generic Merlin mount.
Lastly head speed... I've always used the head on normal speed... can I be using it in fast mode? I just didn't want to wear it out?
The fast/normal/slow mode options only apply when moving the head manually using the arrow keys, not when shooting automatically.