Okay, I am trying to make a new map and I created the blank map, munged it, then tested it to make sure it worked. It did so I deceided to make some new trooper skins.I put the REP side folder in my map side folder and edited the TGA file I wanted in GIMP 2 and replaced the old one.
I edited the MAPc_con.lua script file readdata line to ("dc:side\\rep.lvl" (using notepad), munged the map (amking sure to load the rep side) and when it finished it opened a text document with lots of warnings, but no errors. I then started BFII and started my map on clone wars conquest mode and it was in the loading screen about 1/3 of the way done the it crashed to my desktop.
Ive tried everything I can think of even using the unmodified rep side but I still have this issue.

Any help would be greatly appreciated.

Can you post the error log?

To get the error log:
Copy the BF2_modtools.exe from the main BF2_modtools folder and paste it in the same folder as your battlefront2.exe, usually ...\LucasArts\Star Wars Battlefront II\GameData. Then you can launch BF2_modtools.exe and play your map to get a BFront2.log located in that same folder.
Note to Vista users:
If you can't find your BFront2.log it may be saved to this location: C:\Users\<username>\AppData\Local\VirtualStore\Program Files\LucasArts\Star Wars Battlefront II\GameData
Or click, Play the map with the BF2_modtools.exe, then post the error log.

did you copy the common side as well as the rep side?

Here is the BFII log:



EDIT
I tried adding the common folder and when I ran the map It worked, but used all default sides.

v To mswf, thanks for the welcome and telling me how to put code in another box. I also had no idea about the double post rule, thaks for telling me.

I can't help you with your problem, but here's what I can do:
Nitro_byrn; Welcome to Gametoast. For your convenience, I'd advise you to read the rules, which can be found by clicking on "profile" in the top of the page (do read them, they're different from others.) Also, you can post long lists of codes between these tags: .[.code.].[./code.]. (without the dots, obviously), so you can view it more easily. Also there's an edit button on the down-right corner of your posts that you can use instead of double posting. (it's one of those rules)

I hope you enjoy your stay, happy modding

Please post your LUA, so we can look over it.