CAD Shift After Alignment

CAD Shift After Alignment

Hello,
i am running into an issue that i am hoping to get some help with. I have been running a program fine for a while and then all of a sudden i have been getting a lot of collision into my part. I believe the problem i am having is after my alignment my CAD shifts and then the CMM thinks the part is in a different location than it really is. My alignment consist of an RPS alignment that uses 4 points for datum A plane, a circle for datum B (origin) , and a slot for datum C (align). I think what the problem might be is that datum B and C are not in line with each other so when i perform alignment it rotates my CAD model. It also makes all my other features seem visually way off in the display. Not sure what the best way to go about fixing this. Any Help?