[seafarer]

Are you running Vista? If so, JSGME actually cannot write the files to the proper "real" directory in "program files" because UAC in Vista blocks that. Instead, UAC causes JSGME to write them to the SHIV folder buried deep down in the hidden "AppData" directory in your user's directory space. Of course, the SHIV binary never sees them there, because it is not Vista/UAC aware, so it goes on loading the ubisoft default settings and controls.

The solution, I've found, is to install SHIV, JSGME, mods, everything, in a directory in my users area (in my case "games\Ubisoft\SHIV"), which bypasses the UAC system (which only controls who/what writes to "program files"). Just change the SHIV default directory during the install, and point it anywhere OTHER than "prgram files".

P.S. If you decide to reinstall outside of "program files", first uninstall SHIV using the control panel tool. Then, also, enable viewing hidden files in your user space, search down the "AppData" directory and delete any and all directories related to SHIV. Then re-install SHIV into the directory of your choice, just outside of "program files" This is recommended for any mod'able program/game installation in Vista (actually, I put everything that did not come preinstalled on my computer in aptly named directories outside of "program files".