Mmmmmmm. Jldjs has a bad ship in the museum, Moonlight does not. That means they have two different base game installations.
The team had that problem early on until we did some research and came up with a bulletproof anti-corruption strategy. Please see
this thread to see the results of our crisis. If you do what it says, you will always have a rock solid base of guaranteed virgin stock game files to install FOTRSU into.
We've found that game corruption is absolutely impossible to avoid when working with 3.6 GB of monster mod. You should regularly uninstall all mods with JSGME and compare game files with a shapshot made when you are 100% sure you have pristeen stock files. When the snapshot says there are differences, do the 10 minute procedure.
Your save game files are preserved. Just reinstall your mods, start SH4, reload your save and play as if nothing had ever happened. Soon we will have an SH4 Anti-Corruption Toolkit, SHACT, to automate the process.