What brand is it? I have two giant batteries-
1) Seido 3400mAh Platinum 2x battery
2) Random Chinese 3500mAh battery.
Guess which one actually lasts? The Seido. If it's a cheap brand, it's more than likely going to not work properly. If it is a nice battery, it more than likely just needs to be cycled a couple of times.
When I got my Seido, I turned it off, charged it for 12 hours, and then started using it. Much to my surprise, it drained to 60% in just a couple of hours. Kept using it normally, and when it got to 4%, it stuck there. Eventually, I resorted to playing a looped Nyan Cat video with the brightness all the way up and all the radios on, and Maps running. Took almost two hours of that to finally get it to shut off. After about a week, it started reporting the correct percentage. Now it lasts close to 6 hours screen on with radios running the entire day. Easily the entire day normally.
Also, AOSP ROMs read battery wrong sometimes for me. Try rebooting once and see whether it changes.