is there any way to stop visual munge from closing off door ways and messing up the geometry so you cant walk over something without falling through?

msh.option file that contains -donotmergecollision

It's in the misc_documentation.doc if people bothered to actually read the docs, though I do admit, it's not explained in there.
On that note, -kcollision and -removeverticesonmerge aren't explained either.

what is -kcollision?

... i had -donotmergecollisions in instead of -donotmergecollision