I can help you there.
I have Windows 7 64-bit, so I've had a lot of quirks to deal with. My recommendation? Stop using VisualMunge to munge your files. It's really easy to do it manually, and then copy all the files over. I'll write up a mini-tutorial on everything you need to munge (in the next few minutes), and how to set up your hierarchy in your addon folder properly.
-EDIT-
This tutorial will be a little sloppy since I'm helping my mom out at the hospital right now and I have limited time.
This tutorial assumes you have your Mod Project Folder created already and you have some basic modding knowledge. Please ask away if you have any questions I will be more than glad to help. I'm not going to teach you how to mod, just how to manually munge your files and copy them over manually.
Okay, first off let us make sure you will have no "shadow files" as I call them. See, my Windows 7 64-Bit computer has this funny little quirk that I'm bettings yours does as well. Alright now, go to
C:\Users\[username]\AppData\Local\VirtualStore\Program Files (x86)\LucasArts\Star Wars Battlefront II\GameData and delete the "Addon" folder if it exists. See for some reason, it wants to put some of the munged files here instead of their proper place causing lots of issues.
Alright now, let's start simple and create our Addon Folder for the mod. We shall refer to the Mod ID as ABC for the duration of this tutorial, replace all instances with your Mod's ID.
1) Go to
C:\Program Files (x86)\LucasArts\Star Wars Battlefront II\GameData\addon and create a folder there called ABC (if it doesn't exist already).
2) Inside this ABC folder I want you to create a folder called Data.
3) Inside the Data folder, I want you to create a folder called _LVL_PC.
Congrats! You now have the basic folder setup each and every mod has to have. Any new folders added will depend on the type and scale of your mod. Let's just assume you are making a map for this tutorial.
4) Inside the _LVL_PC folder lets create the map folder, in this case the folder will be your Map's ID. Again lets just call it ABC.
5) Now let's get mungeing. First off head to
C:\BF2_ModTools\data_ABC\_BUILD\Common and double click munge.bat in the folder. This munges your mission scripts, your localiztions, your common files, and your ingame. It's the most important of all the munges. Matter of fact, you can NOT munge your munge untill your Common has been munged at least once.
6) Now let's munge your map. Go to
C:\BF2_ModTools\data_ABC\_BUILD\Worlds\ABC, now right click the munge.bat and click edit. I should look like this,
Mr. Mungey wrote:@call ..\munge_world.bat YAV %1
Now change it to reflect your map's ID. In this case,
Mr. Mungey wrote:@call ..\munge_world.bat ABC %1
Now save and exit. Then double click it to run it.
7) Now let's say you have custom sides in this map as well? Let's assume for this tutorial we shall say you are replacing the Republic side in your map with a custom on of your own. Let's go to
C:\BF2_ModTools\data_ABC\_BUILD\Sides\REP and double click the munge.bat there.

Now where have all these munged files gone? Head on over to
C:\BF2_ModTools\data_ABC\_LVL_PC. You'll see all your files there. I'm sure you know them but let's go over them really quick, the important ones anyway. The Mission.lvl contains your mission Lua scripts, very important. Your core.lvl has all the localiztions, also important. Inside the ABC folder is your map we munged. Inside the SIDE folder is your custom Republic side. Now time to start copying, or rather cutting them if that's what you prefer(I prefer it myself anyway). Copy/Cut both the Mission.lvl and the Core.lvl to your
C:\Users\[username]\AppData\Local\VirtualStore\Program Files (x86)\LucasArts\Star Wars Battlefront II\GameData\addon\ABC\data\_LVL_PC (that you had created in step 3).
9) Now lets Copy/Cut both the SIDE folder and the ABC folder from
C:\BF2_ModTools\data_ABC\_LVL_PC into the same
C:\Users\[username]\AppData\Local\VirtualStore\Program Files (x86)\LucasArts\Star Wars Battlefront II\GameData\addon\ABC\data\_LVL_PC folder as before. You're almost done, one last important thing to do.
10) Now lets go to
C:\BF2_ModTools\data_ABC\addme and double click mungeAddme.bat to run it as before. Go into
C:\BF2_ModTools\data_ABC\addme\munged and copy the addme.script to C:\Users\[username]\AppData\Local\VirtualStore\Program Files (x86)\LucasArts\Star Wars Battlefront II\GameData\addon\ABC.
11) Now as long as the munge is working properlly, which depends on whether the Vista Fix was installed properlly or not, you're all done. Test!
Note: Every time you update your mission Luas or your Localizations you need to munge the Common again and copy the files over as before. Same goes for any side, map, addme, etc changes.
This may seem really complicated, but
trust me, if
I can do it you
can do it. You get used to doing it really quick and it's personally a lot better than using VisualMunge. I still use VM, but only for creating Project Folders.
Let me know if you have any questions, I or any of my modding associates will be happy to answer your question(s).