CCR - Difference in Contents for order

We have a large number (16,000) of difference in contents errors for planned orders when I run CCR. When I try to send from APO to R/3 or visa versa, the changes don't go through most of the time. I've found that if I make a change to the order in R/3, the order will reconcile itself between the two systems.

SAP initially recommended changes to CP3 so that the APO date always overrides R/3 order date changes. We use SNP to do long term planning for our plants and use R/3 (MF50 Order Dispatching) to schedule the orders in the short term (2 weeks out) so this won't work for us. I tested it and it ignores all of the dispatching we do.

Has anyone else seen this? I can't help but wonder if its a bad design on our part to use APO to do part of the planning and R/3 to do the rest. Regardless, I would still hope that order changes in either system would flow seamlessly back and forth.

Thanks for any help!