Are you using rechargeables or regular?
I'm using regular ones. It turned out that the problem wasn't the batteries, it was the OS. It seems that once the last update came out, 10.7.4 (have you updated your software?), the problem solved itself.
My battery status for both magic mouse and apple wireless keyboard (2 batteries), now shows the correct status.
It doesn't stay "stuck" on 100 or 99%, thusly, the reason I had the problem was b/c I was under the impression that I had a full battery when I did not.
Prior to the update, I downloaded the Mighty Monitor Widget
http://www.apple.com/downloads/dashboard/status/mightymonitor.html
which always gave me the accurate readings.
Try this: put new batteries in and see if your mouse starts to function correctly. If so, then you are also getting an inaccurate reading.
Or...download the widget and see how low your CURRENT batteries are 😉