I was just made aware of the incompatibility and looked through and tested some stuff, and as nearly as I can tell, the main incompatibility is as follows:
1. The custom UI mod makes creating a new gui object take about 16x longer than before
2. TMBI uses an inefficient, but universal refresh system that deletes and recreates most of the interface to handle any sort of update instead of writing dozens of little mini refresh codes for all the different possible ways the inventory can be changed, which worked like a charm as long as there were less than 80 rows of bricks before.
Since it really isn't possible for the custom UI mod to become more efficient, the way torque works n stuff, I guess the duty falls on me to do something about making a less flexible but more efficient update system in TMBI.