So I have two problems.
One, I have an old map that I use as a test map that has decided to stop updating.
Let's say I put in an object from the common folder, save the map, close ZE and munge. When I run the map, no changes have been made.
Now I might say that I did something in the past to mess up the map, but my second problem seems to suggest otherwise.
When this map stopped working I decided to just create a new test map. I run the visualmunge from data/_Build, make my new map, and everything seems fine. I put an object in this map, munged, ran the map, and it crashed saying that it could not find/read mission.lua. I thought maybe a clean would help and when I cleaned pressed clean in visualmunge, I got this in the output box: I decided to again create a new map. This time, right after creating the map, I went to clean and it did the same as above, for that matter, everything about this new map failed the same way as the previous.
Right now I'm thinking that somehow my visualmunge has gotten corrupted (is that possible?), so if anyone else has any ideas, I would appreciate it.

VisualMunge has a lot of glitches. The clean button is unreliable. Do a manual clean and then try munging your original test map and see if it works.

Thanks, the manual clean worked for my previous test map (or at least I assumed it did because it's now crashing when I start it, meaning my edits are kicking in).
Meanwhile, for the other problem, it seems to have developed a bit more. The same things happen when I create a map as before, so I thought to look into a manual clean right off the bat (or should I say, after I've munged the map once). This is where I noticed that even though visualmunge said that it had munged (I double checked) the .../***/MUNGED folders and the .../data_***/_LVL_PC folder never showed up for me to manual clean out of. Any ideas?