I'm no Vista expert, but I do remember reading that many mods are set up to look for their component specifically in the installation folders that are found in Windows and Vista has slightly different paths to the mod folder. Not sure, but that might be a direction to look.
Also, I installed Civ IV Gold and could not load a mod (they always crashed), turned out that there was something wrong with my installation cd's. I loaded Civ IV with a regular version and everything was fine. Can you load the mods that come with the game? If not you know it's not an installation error on your part with the new mods, but something quirky with either Vista and path names or with your game installation.
Wish I could be more help, but that's all that comes to mind. I spent many hours troubleshooting to get my Civ IV to play mods, in fact ended up reformatting my drives and reinstalling Windows XP (by the time I messed with everything I'd also messed up my registry, or it was before I started, who knows?). A completely clean install with the regular version of Civ IV worked perfectly. It was worth it though, I play Rise of Mankind multiplayer with my friends and we have had many hours of enjoyable gameplay!