Maybe it's something else draining the battery, like the wi-fi being on?
Nope, wifi is off and as a said, its weird because psx4all had the same behavior with hours of battery as the other emulators
With psx4all, did you have sound enabled, along with XA and CDDA audio? If a game is streaming music from CD, as most do, it will read a lot of data from SD, which contributes to power drain. Depending on the game, one might read a lot more from 'CD' than another. However, once the data has been read once and, let's say, the music loops, it will be reading it from disk cache.
One thing I'm going to be working on that might help is adding a volume-setting to the frontend. The new SPU plugin we use has an overall volume setting that's set at 75% volume by default (PCSX Rearmed's default setting), but allowing it to be set to 100% would allow a lower volume setting on the GCW Zero's master mixer (what you control with power slider up/down).