[mookiemookie]

JScones can tell you better, but the way I believe that the JSGME works is this:

When you activate a mod, the program makes a copy of the original files that the mod changes. When you deactivate a mod, the program overwrites the modified files with the original backups. Since you've patched SH4 in between activating and deactivating your mods, the original backup files may not be current anymore as they could be files affected by the 1.2 patch.

I would reinstall to be on the safe side.