I had the same problem when I was setting up my vanilla for when my download finished. It's due to not deleting the SH3 directory after deleting the program. A re-delete and a few quick tosses into the recycling bin, and everything works awesomely.
You know...it's a testament to the hard work of the modders when it's harder to install the vanilla game and it's upgrades than it is the mod.
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