I was compiling one of our projects to get it ready for an updated release and ran into an odd issue. Everything looked good on initial load but the page started throwing errors pretty much immediately. So I started digging around and saw that the JSB file that previously worked fine was only outputting 3 stores and their associated models. Whaa?
Turns out the developer had put a stores property with those 3 stores in the application definition function. It worked fine when loading everything 'manually' but when it came to the compile process it saw that stores property and apparently just STOPPED. Very weird.
So to fix it I just moved the stores definition to the applicable Controller and everything started working again. Very weird behavior but hey at least it was an easy fix (once I knew what the problem was of course!)