[DrBeast]

This little detail may sometimes slip our mind, be it modders who are making their mods JSGME-ready, or users that install those mods. What does this mean? I'll elaborate with an example:

Let's say we have mod A, which is structured as thus: data\Library\AI_Sensors.dat. What does it do? It replaces the AI_Sensors.dat file, found in the game's Data\Library directory. We install this mod, JSGME keeps a back-up of the original (core game) file.
Now, we install another mod that changes the AI_Sensors.dat, mod B, which has this file structure: Data\Library\AI_Sensors.dat (notice the capital D in Data). What should happen? JSGME should issue a warning that mod B contains a file that exists in mod A, correct? Well, this won't happen! Instead, it'll quietly overwrite the file from mod A, and keep a backup of mod A's file. "Nothing to worry about, we just don't get a warning", you might say. Correct, but what happens if we disable mod A? Normally, JSGME would tell us that we'll have to disable mod B first, as it has altered the same file. It won't do that! Instead, it'll remove the AI_Sensors.dat of mod B and revert to the game's original file, essentially disabling both mod A and B. But, if you then proceed to disable mod B, it will revert to the file from mod A! You can see how this can mess up your original data, yes?
However, if you take the correct route and disable mod B before mod A, you're trouble-free. JSGME will revert to the correct backups all the time.

What needs to be done?
Well, modders should check and be sure that the file structure they're following is an exact copy of the core game's file structure, down to the letter. Mod users should check to see if the file structure is indeed correct. This might save you from needless reinstalls and frustration. Also, when you're disabling mods, make sure to disable them from the bottom up, to avoid any foul-ups of your core game's files.

Hope this helps, happy hunting!

Edit: Guys...disregard all this and go grab the newest version of JSGME (2.0.1). It solves this problem. I thought 2.0.0, which I had installed, was the latest version, but I guess I had a brain-fart and forgot there was a newer version released a few days after I got that one. My apologies for spreading false information.