In a 16 note pattern where a kick is 4 to the floor and a bass synth is playing on ever &. 1, &, 2, &, 3, & 4. or
1 (kick) 2, 3(Bass), 4 : 5(kick), 6, 7 (bass), 8 : 9 (Kick), 10, 11 (bass) 12 : 13 (Kick), 14, 15 (bass), 16. 
Yeah the kick and the bass are slapped right ontop of each other and in order to have the bass play on every down beat I must offset the kicks to the right by a whole 8th note. Seriously what the hay. Even when I try to change the "loop" start and end times, it doesn't do anything, like nothing at all. Can I not use midi to sync Nible Drums or is the only way to get any use out of this is to try to use midi to make a pattern, record it out, and just use the recorded out audio to resync everything which is a lot of work given all my other instruments, hardware and VST, work flawlessly.

Sorry for the late response. I'm not entirely sure what you're trying to do. Are you trying to use the Loop feature to loop your sample? There's currently no synced time option in the looping section, so that could explain the inaccuracy you might be seeing. In general I would suggest you program the midi in the way that you want the sample to play.