When I was making the Reboot, I didn't scrap the original code just add some code... I did not erase the original "continue" SEXP. I realized that in the latest FSO built, it will cause a problem. Probably beause the latest CPUs, them with multi cores, multi threads are no longer linear in processing things.
It's defintely not a parallel processing thing, sexp processing doesn't do that and it'd take a spectacular screwup if it ever does in a way that would create this problem.
But there have been changes, some intentional and some not, that can break things like this. Using the 3.7.2 engine is definitely the right thing to do unless that version is entirely unusable for you for some reason. That goes for any older mod, really, of course for whatever version they were made for.