Default Weird Battery Status Issue

Ok if your running a custom rom that may have been tweaked one way or another to make it go into deep sleep when the screens off would that effect the battery status and give a bad read? Because I'm at 72% with a battery read at 3h 33m 15 sec. I had the phone off a 100% charge for about 2 and a half hours with light use. When i refresh it it only goes up a few sec. at a time. Anyone ever had this issue and might have a idea what is the cause?
Samsung - Galaxy S4
SPH-L720 (Sprint)
Android 4.4.2 NAE Kit Kat
Negalite Rom NAE-x r6
Negalite Kernel NAE-r50
Framework Animation Mod N7 Port
Philz Touch Recovery
A.i. Type Keyboard