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.
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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:
rm /data/system/batterystats.bin
This will prevent you from seeing any discrepancies in the usage of your battery & the battery stats.
2) Wipe the dalvik cache:
rm /data/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:
reboot
This is what causes the kernel to re-calibrate your battery, when the phone is rebooted after a full charge.

SudoSURoot
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batterystats.bin
is not related at all (yeah, the good old calibration myth). That file just holds statistics on how apps were using the battery – not how the battery was depleted. Secondly: could you please explain what the Dalvik cache should have to do with it – and if it really is related (which I doubt), what would be the equivalent with ART (Android 5+)? Third: For a calibration, the battery must be "depleted" first (discharged to ~5..10%), as otherwise there won't be a complete charging cycle. – Izzy May 08 '15 at 08:57batterystats.bin
: find it explained by Google developer Dianne Hackborne :) – Izzy May 08 '15 at 09:02