strixo: All the weidu executables should be run from within the game directory you'd like to modify. But hold on, are you using EasyTutu? Easytutu includes a fixpack. I don't think I've ever even used the BG2 fixpack with Easytutu.
Quinch: -facepalms-
I'll reinstall Tutu and check...
{prepares to feel like a dolt}
You will want to install this as well, somewhere right before tweaks.
http://www.mediafire.com/?8i2qaa6z8zxilkm Courtesty of Ascension64 @ SHS, courtesy of Thiev here. This fixes a bug that has not been yet addressed in EasyTutu. Ascension64 is also an author of the BGT mega-mod, and the fix is integrated there...however, EasyTutu hasn't been (AFAIK) updated so regularly.
DavidW slipped the same fix into his 'core fixes" of SCS1 @ G3, but I doubt you'll want to try that mod for some time.
edit: why are you reinstalling? If you want to see what mods/tweaks have/have not been succesfully installed, open weidu.log with notepad in your game directory. Weidu does not generally do "broken" installs. If a tweak/mod is unsucessful, unless you terminate the application prematurely, I believe it restores files from a backup directory.
edit2: and if you are concerned a mod/tweak may be corrupted, just re-execute the tweak/mod using the weidu executable. It will prompt to reintall/uninstall.