So I think something is broken with the BWS tool. I have tried clean installs of both the game and the tool and the BG2EE EET install wont let me progress. I have used this tool to success the previous day and got the whole game and mods to work correctly, minus Colours of Infinity not working do to an Unix override error. Before you ask I don't have the debug files from the installs last night, I foolishly deleted everything thinking it was something on my end and I was just using the tool wrong. This afternoon when I started to try again it keeps telling me I am missing a bunch of area files from BG1EE and will not let me continue in the tool when I specify the directories. I have started the game with a clean install, made saves and so forth. The games run just fine in the none drive directory so I know I am not missing area files. At this point I don't know what to do.
Just chiming in to say that I've had the exact same issue. Was poking around in BWS last night. Started it up again today and was getting errors about BG2EE not being correct in my user config ini folder.
Fresh installed BGEE and BG2EE - also downloaded a second copy of BWS just to be safe. Ran it - and my BG2EE/BGEET install option doesnt appear to work properly. There's a "0" where BG2EE normally should be, and when I select the install directory for BGEE itself, I get an error that I have a whole host of missing error files.
Edit - side note: When I select BWS for only BGEE and not the BG2EE/EET option, it seems like it works fine.