Turns out the issue a majority of the time it was due to warp spaces using odd numbered floating point registers, updating events to use even numbered ones made the hardware happy.
For added context, I'm using an everdrive x7 here on an unmodified console. Most boards I've tried work flawlessly in emulators, but have a problem on getting stuck on events and happening space transitions. For example, big boo's blackhole boardwalk gets stuck on the question mark cutscene when...