RS, check out this post of mine. I speak about making a JSGME compatible mod. And what I am getting at with you is make sure the mods you have downloaded have the right file structure. Some modders put their mods in a separate folder, so you have to first take the mod out of the folder you unzipped and then place it in JSGME, then activate. And best to be in port when doing this for most.
Here is that link:
http://www.subsim.com/radioroom/showpost.php?p=2187070