I do not run my mods from the jsgme mod folder. I keep them in the silent hunter mod folder only. This avoids errors.
JSGME is in my root silent hunter folder with its icon on the deck top. I do not use it for any other game so putting it in the silent hunter folder works more efficiently.
Even if I did have other games I used it for I could simply place a separate copy of JSGME in each game root folder and have a separate icon for each on the desktop. That way each desktop icon points only to that games mod folder and none others and not JSGME.
Check this for proper installation of JSGME:
http://www.subsim.com/radioroom/showthread.php?t=180046
And here for tips and tricks:
http://www.subsim.com/radioroom/showthread.php?t=204593