I have a rooted Galaxy Nexus (maguro) runnung an AOSP 4.4.4 rom and Franko.Kernel r396. I also have Gravity Box installed and have replaced the battery percent icon with the circle battery. As far as I can tell, these are the important factors relating to my issue. I have an app that shows battery voltage next to percent, and at 50% the voltage is 3600, but from what I've seen 3600 is supposed to be zero. If my battery falls below 50%, I have to keep my screen off or the phone dies instantly with no warning.
Let me simplify since I see we have debaters.
You should calibrate your battery:
After you use your battery, as low as it will go, below 20%. Plug it into A/C Power until it is definitely fully charged. Wait an extra 20 minutes to make sure that it is fully charged. Then you need to:
1) Remove the battery stats file:
This will prevent you from seeing any discrepancies in the usage of your battery & the battery stats.
2) Wipe the dalvik cache:
You stated that an app is showing your voltage levels as being correct, so you may need the app's cache cleared.
3) Then Reboot:
This is what causes the kernel to re-calibrate your battery, when the phone is rebooted after a full charge.