Because you just KNOW that whenever you release some nice new shiny thing of course something's going to go wrong ːsteamfacepalmː
What was happening was that the main storyline missions for the game were getting all DISCOMBOBULATED somehow. But it just didn't make any sense on WHY this was happening, as nothing that usually connects the missions would have gotten affected this way.
Here was the error:
Missions 'Originality Supreme' through 'Cardinal Rule' worked how they should have, and then after the reward screen it directly jumped to a mission that's supposed to take place 5 or 6 later (and without going back to town first, or stopping the reward screen music!). If you won that Peeing Guard mission, it'd time warp you back a few missions but along the line another wrong frame jump would happen until eventually it hit an Intermission early and then took you back to town, where the Evil Dungeon Door (-tm) was permanently closed.
I believe the scientific name for this happenstance is: FUBAR
Do you know what it ended up being? Some giant equation? Some cryptic file action? NOPE. Somehow during the game-making process I happened to accidentally swap a few of the multimedia fusion frames with each other (how'd this happen? It's actually really easy to do if you're not careful enough). So often during the Reward Screen a set Intermission sequence or something else would be called upon by a Frame # ID. And when the frames were swapped around, the game still jumped to that same Frame # ID, only this time it was something completely different and it screwed the pooch big time!
Thanks to 'Deathofcheese' for finding this error and letting me know about it ASAP, and I've since located and fixed everything a few hours ago as well as start a new game from scratch and run through everything to double check the mission sequences (which check out once again).
So it might be a bit embarrassing but I only wish other devs would be so forthcoming with their game's players and not keep them in the dark so much. :JAC_Shemp: