[PepsiCan]

When you run SH4 for the first time, a new folder gets created under My Documents\SH4. It holds duplicates/copies of various .UPC, .CFG and .INI files there that are used by the saved games.

So, when you do not uninstall all your mods before you upgrade to patch 1.3, patch 1.3 will actually overwrite a lot of the files with new, stock game versions. That means that linkage between the mod files get destroyed and you get internal contradictions. As soon as that happens you'll get CTD's (Crash To Desktop).

So, when patching, always uninstall all your mods (and that only works when you used JSGME the right way, from the start, on a stock version of the game) and then patch. If you leave any mod files behind you'll look at a crash.

What may also help, is to delete the My Documents\SH4 folder. If there are any files in there that are not in sync with the files in the main installation folder, then that deletion will resolve any discrepancies. The downside is of course that you lose your saved games.