Could it be the insert that you are using?
I don't think the insert is the problem. The insert is the same one that came with the camera, and I have been using it without a problem since I purchased the camera new a few years ago. I think that something is wrong with the design of the rapid winder I have, maybe one of the gears is too big or out of allignment. Without the rapid winder, my camera works flawlessly. Also, I kind of like turning the rewind crank knob instead of advancing film with the thumb mechanism. It reminds me I'm usung roll film!
I have heard that there are universal grips for the 645, I'm not sure if one can be used with the 645E though. The problem is with the shutter release button on the 645E. Unlike the 645J, the shutter release button on the 645E does not protrude from the body as much. On the 645E the button is almost flat against the body, so when you place the 645J grip on it, there is a small gap between theshutter release button and the firing mechanism of the grip.
I thought about getting 645J grip, drilling a small hole on the tiny metal surface that is supposed to touch the shutter release button, and adding some sort of small rubber extension so it touches the shutter release button. Of course, it would be a whole lot easier if there were a grip out there that was already designed to fit the 645E...