In addition to the controller problem, you may also be having a problem with the controller. I'm trying to think of an easy way to test out whether that is the problem.
I was going to suggest you short the 5v pins on the throttle connection, but I don't know how that will react. Perhaps there is a safty mechanism that prevents that. It's also possible that full voltage is 0% throttle, and low voltage is 100% throttle. Alternatively, if you have a spare throttle (e.g, from your first throttle), I would try connecting that.
The only other problem I see could be the controller. However, it's cheaper to try out the throttle. I'd be careful about connecting batteries directly to the motor- if you're using Lipo you could really pump some high current through it and burn things out in short order :p
I would wait on seeing if anyone else knows if shorting the pins corresponding with the throttle signal will give 100% power.
New to endless-sphere? Notice a lot of signatures recommending Ebike.ca? That's because it's the best place for a quality and manageable, (but still 'real'), first build. Justin is a solid supporter of electric bike development, and a good source of equipment.
My hat off a thousand times to the green people that effectively run this forum. The ES Mods are superb.