Problem with Installing mods

I'm having trouble with my sins mods.  THis is what happened:

I downloaded a mod for Sins when it was v 1.05.  I wrongly copied and pasted the file folders (Particles, Game info, etc., not the individual files themselves) directly into the Mods folder instead of extracting the whole thing.  I created a new folder (named after the mod) and moved the files in, but when I loaded up SINS it still showed the individual folders instead of the single mod (I was using the 'real' capital ships mod).

Now, I deleted that, and downloaded the Star Trek mod, and I updated SINS to the latest version, but those old Mod folders are still theres (even though they've been deleted) and my new mod isn't showing up.  Help please!  XP, btw