What JSGME does is save the copies of files that a given mod will overwrite before it does the overwriting, so that it can "go back" to the previous state when you de-activate a mod. "Bigger Better Protractors" is a small mod that only alters the tools you see on the NavMap, so if you add a mod on top of it that also alters the same area, it overwrites "Bigger Better Protractors", you do lose that mod's functionality. That is the way JSGME works. It will warn you of file over-writes and folders previously altered or created. Depending upon what mods you are using, you could activate the other mod(s) first, and then activate "Bigger Better Protractors" last, since that is all it does, is alter those NavMap tools.
If you want to, list the mods that you want to have running, and someone will have some advice on the activation order, and if there is anything to be aware of, or maybe not needed in your list. Also, be aware that if the SH4 game is installed in a "Program Files" folder in Windows, that activating a mod will result in Windows rolling back the edits that JSGME does, since Windows "protects" those folders from "un-authorized" alteration, and neither you nor JSGME are "registered" with Windows as "authorized", even though neither of you are "bad characters"... but that's Windows. You would need to have the game installed in a folder you create. Let us know where you have the game installed also, please.
