When I built a ROM with the same SYS in both OMJ and Mystery, the number of modules listed in visualkitchen was approximately the same (around 460).
I was trying to figure out what else could be wrong. I noticed in visual kitchen, at the top where you select device, sys version, xip version, ROM name, etc; if I chose 24001 or whatever version in the drop down box for XIP before doing so for SYS, then the ROM would not boot. If I chose the version in SYS box before XIP box, then it did work.
Here's waht I mean:
