Did not see this addressed- sorry if it is a repeat-just thought it might help someone out there.
I have an Xbox thats brand new and I was using a Nyco rechargeable battery - first time I took it out and placed it on the charger it refused to sync when I put it back in the controller. After some tooling around we discovered that the newer controllers we had - including one we thought was broken were not syncing when using the Nyco. Using double A's synced right up and I just got a new set of Xbox rechargeables to work with it. The double A's do tend to die out fast though on my new controller, but the Xbox batteries work perfectly. The Nyco batteries even went so far as to cause lag when trying to connect with the charge and play cables. The older controller that is about a year and a half old works just fine with the Nyco batteries.
This was incredibly irritating for me when it happened, and if we had not had another "problem" controller in the house as well as an older one we would have never noticed what it was doing. Just a bit of info for those who are at the end of their rope ;p