That's odd. It sounds like the game was patched incorrectly.
Check to make sure you have a file called "pak2.pk3" inside of your MOH\mainta\ folder. This is the files for Malta.
My advice would be to totally uninstall MOH and SH. Move your maps, mods and skins to a temp folder, then use this:
http://mohaa.xgshosting.com/joe/installguide.htm
Last, install the V1.11 patch for MOH, and the 2.11 patch for SH, then boot MOH:SH, and see if Malta loads.