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I wasn't sure wether to put this here or in the modding forum, but anyway, here goes:
I have made a unit model in xsi and followed all the tutorials I could find to make sure I got it right, but after I had exported, and had come to the munging stage it does not munge my unit properly. I checked in my _BUILD\Sides\REP2\MUNGED\PC folder and found that instead of where a model's req file usually has something like: Mine just said: and nothing else. Does anyone know why this would happen?

Thats about what munged model reqs are supposed to look like.

Delete the model req and remunge, this will cause Visual Munge to re-Munge it, like you had cleaned, but without having to re-munge everything else.

Also does the unit work in game, ect, could you give some more detail about that sort of thing?

No the unit does not work in game, it did before my custom model though...
Here is my unge log: and my game log: As you can see the only unusual message severity 3 is the model one, which is meaning that it is not munging properly...

Ok munge log says that it didn't munge right, and the game log says you have a sound error, and that the concerned unit is missing it's geometry, called all_inf_ghilli
When the model you are munging is called all_inf_ghillie. Fix that typo first.

When you munge the model, does Visual Munge slow down? First off, if it does, don't stop it, let it keep going till the cows come home.

If you still can't get it to work, there is another possibility, make a .msh.option for the soldier mesh, and add the line: -donotmergecollisions

About the typo bit, the entity part of the missing geometry bit is talking about my odf (which is called all_inf_ghilli).
it is only the model that is called all_inf_ghillie, and this is referenced right everywhere i think, but i'll check again just to make sure.
I'll try your second method aswell and see if that works. I'll edit this after i have tried.

Do a manual clean and re-munge. You model didn't munge correctly for whatever reason. Once you manual clean you'll know more.

@Tean: I've tried manual cleaning and visualmunge cleaning tons of times, and the munge log i posted is the same every time...

Then you probably still have something misspelled, check the msh name of your new unit and see if it matches the name that you're calling in that unit's ODF on the GeometryName = "" line.

calling in that unit's ODF on the GeometryName = "" line.

sorry if I am bumping this topic but is a geometryName a mesh or skin or both?

The .msh only, which should be localted into the msh folder. The msh itself will link to the textures/skins/tgas, also place those in the msh folder. This can be found in the jedi creation doc. You should really read that; it explains all basics about sides!