Are you POSITIVE the motor is the issue? An issue with wiring will cause that... and the on-off switch on that box is the first place I would look. (I mean the one on the side of the box... although the actual switch that the lid presses can give you a headache too... BTDT)
(I have this box and had a similar symptom... improving the wire connections made a HUGE difference.)
And yes, that box will work fine with Lipos. My bud has one with a single 4s LiPo... shows about 16v fully charged, and I think that box would start a top fuel dragster!