If you had no problems before changing the string and cables then I suggest that is causing the problem.

I'm not familiar w/ the binary cams system but I would check and measure everything. Especially TILLER.
I had the same problem just yesterday. I had changed the string and cables(on a Trykon)and since then could not get it paper tuned, and arrow flight was inconsistent. Even though the ATA,brace,and cam timingmarks were correct, the tiller was way off. The top limb was out by 1/4" an inch.

I know a Trykon is not at all similar to your Alligence ,BUT,they are both 2 cam bows and as such tiller needs to be even top and bottom so the limbs and cams mirror each other on release.
One or the other cam rotating before the other will cause the problems you are speaking of.

Check it out and see.