BINGO! I think been has really nailed it here. The "Center Point" is different on various types of guitars. Finding that spot, and learning to play in the "sweet spot" is often tough when switching between guitars that have different center points of balance.
I play a lot of "Super Strat" shapes, and most of them have similar balance. When I switch to my Les Paul shaped Minarik, I"m thrown off, bad. Takes me bit of playing to get used to it. It's very different than my ibanez guitars or my fretlight super strat.
Your body will get used to it, but don't try to play your hardest/most complex riffs just after switching. Until you practice doing the switch and playing the riffs. Just jumping in during practice can make you feel like you've lost control of your hands
Todd
Ah, I know why.. it's because the centre of balance for the body is in a different place. I've experienced this but the other way around. If I try to play an SG with a strap, stood up it feels weird to me. The picking hand is in a different place and the whole thing just feels alien.
In theory, playing the Jackson (I have one) will feel like your picking hand is further back, so your elbow is out further and your fretting arm should feel closer to you ?
We all get this when we pick up guitars which have different weight balances and shapes. It's totally normal. You just have to get used to playing it. Just try to get a strap height that allows you to articulate licks properly with your fretting hand and doesn't make your picking hand angle change