I haven't been able to get multiple copies of SH3 working with Steam for the same reason, I think Steam tweaks the .exe file, so I'm ordering an actual CD copy.
However, for now I'm running SH3 Commander, GWX and other mod soup with no issues at all other than some occasional minor bugs with Commander that I'm sure are Steam related. Every mod I've tried goes on fine through JSGME.
Get JSGME, put it in the right SH3 directory (steamapps/common/SH3 usually), put the mods in the MODS folder in that directory. Some mods with an installer, GWX for instance, need to be pointed at the correct directory to work or you'll get some oddball error message.
Works like a champ, Steam is not the fun eating depth charge of a sub killer some folks make it out to be. I'm getting the hard copy because I want to do multiple installs to try out different mod sets and it is cheap.
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