I have experienced the same from many years of mousing. I've changed hands and mouse left handed at work, right handed at home. I also have wrist support mouse mat (theres a bump of some thing spongy that forces you to keep your wrist fairly straight instead of resting on the table top and your hand and fingers arching up over the mouse. I have a similer thing along the front of my keyboard to do the same thing when typing), it seems to assist.
Forgot to add, I don't have any trouble getting confused changing mousing hands... however it's funny watching others try to drive my left handed mouse right handed... the pop-up context menu gets a workout!