Switching regulator enable pin low, but output isn't fully off. Why?
Yep, that voltage makes sense -- look at U1. It's a non-synchronous converter; even if it's "off", you will see a diode drop on 5V from VBATT because current can flow through the inductor and through the diode with nothing stopping it. In a synchronous converter, that diode may be a switch (MOSFET) which would prevent the issue you are seeing.

EDIT: Here's the illustration (it took me embarrassingly long to find a MSPaint equivalent on OS X):



You'd have to put some kind of switch upstream of the 5V regulator if you want everything fully off on that rail.

As for the 3V3, looking at the data sheet, it appears to be a synchronous converter (even if it wasn't, it's not generally an issue for a buck topology) -- do you perhaps have a different leakage path? Something from 5V onto 3V3? Might need to see more of your schematic to be sure, but from the snippet you've given, the 5V behavior is expected, the 3V3 less so without more info.