Hi, you didn't mention if you're getting the voltage expected on the boost output, so on your circuit the low voltage protect IC will cut the battery from it's B- side, so if your measurement it's from B- to vin (on the boost IC) your always will get your B+ B- (battery) voltage, your measurement should be from B+ to GND, another way to do the measurement it's from the boost output, of course.
If you're still getting this behavior I'll check for a possible bridge between B- to GND, and then maybe a failed mosfet or the protect IC.