Hi
Xapp696, Welcome to SUBSIM
This:
I use JSGME, and name the folders within the MODS folder the exact same as the files that I'm installing
Just a question, you mention above naming folders, when you extract\unzip the mod, it is already named and JSGME ready, no need to re-name. By re-naming a folder you are messing with the JSGME folder\file-path configuration, thus it will not activate. I may be wrong here though, as you mention some other mods you have installed.
Also,
on my sig there is a link to an Illustrated Guide for JSGME, you may want to check it out for future reference.
RDP