The "Save" system is wonky at times... When you change mods, you need to change the Save data folder for all version-to-version changes of FotRSU thus far. This will oftentimes include certain configuration changes. Some mods can be activated while on patrol, but they are few and far between, and if you noticed, Team_Leader changed the next version from a "Possibly compatible" to a "probably not" compatible next-version... It doesn't take much of a change in a mod to do that. If you have a campaign you want to keep, it is best to not mess with the mod configuration, unless it is for something like a flag mod.
Just for clarification, the LAA app is independent, and has nothing to do with SH4.exe. When you run LAA and "enable" SH4.exe, all you are doing is flipping a couple of bits in the SH4.exe executable file's "header" that lets Windows know that it (SH4.exe) can access more than 2 gig of RAM. Once the SH4.exe is replaced with a 'pristine' copy, it no longer has those bits flipped and will need LAA run against it again.
So, when you go from beta to the full release, you need a 'pristine' copy of FotRSU. You need to run MulitSH4 next if you are going to use it. Then LAA. You can enable the new mod most anywhere after the 'pristine' is brought in. But you must not fail to empty the Save game folder, else you pollute the Saves that you already have, and end up with a strange mess sometimes. When in doubt, clean the Save folder. From the way you describe your situation, the "Save" info was probably already corrupt from not having LAA set correctly, so when you do enable LAA, you've got a mess in the folder, and it just kept spreading...
