I ran into a similar type of problem with the 360 pad. At the moment, I'm only using a single 360 pad (I generally only play multiplayer between multiple systems, so I haven't really needed it). I have a wireless adaptor for my PC, however, so I often switch between the two. Well, this causes two problems...
The 360 itself loses track of how much charge is left in the battery and always reports the incorrect amount. More importantly, however, if the controller is drained it becomes more difficult to sync up with a different device. For instance, I wanted to use my 360 yesterday but the pad was in sync with the PC. Unfortunately, it would only power up for 2-3 seconds before dying. That wasn't long enough to hit the "sync" button on the top. When I plug it in with the charge cable, however, that button is hidden so it automatically syncs with the PC. I kept trying to hit the button and quickly plug it in, but that wasn't working. I ended up letting it charge for 10 minutes or so and then switching over to the 360.
If I still had the original battery cover I guess I could have used AA batteries to do it, but I have no clue where that went.
