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Whenever i add a side to my custom map from the original assets folder VisualMunge comes up with about 5 warnings that say Sometimes the units are slow, sometimes they are not, why is this?

that's because the .msh.option doesn't have the -nocollision line in it. the munger automatically generates collision for in game objects, but because they are units, the collision doesn't get used (it uses pre-set collision primitives for units). By slow it means performance will be less, but for units you can ignore this message, it only impacts munge time.

I once tried to add additional gammoreans from jabba's palace into a custom survival map, yet when i munged the finished map, it came up with that error. the gammoreans were slow in game (in terms movement speed). Is that related or just a scripting error i overlooked?

That is because they have a low MaxSpeed value on their odf file