EE Mod Setup Tool Problem - "Please start the game, choose the language..."

Hello all, Would appreciate some help with my install. I was able to install mods to my BG2 - EE game by copying the contents of the SteamApps - BG2EE folder to a folder on my desktop and running EE Mod Setup Tool. Enjoying that playthrough so far. Meanwhile, I am trying to do the same for a different folder, with a different set of mods applied. So I copied the clean install from Steam to a new folder on my desktop, extracted EE Mod Setup Tool to that folder, and tried to do another install. However, when it comes time to download/extract/install the mods, the Tool stops and displays the "Please start the game, choose the language...", error, even if I have made sure that I started an SOA game and already have a save available. Any tips or help would be appreciated. Thank you!