StarTroop: I don't know if you've solved the problem yet, but are you installing BGT before anything else?
BGT should be installed first (with the exception of the Ascension mod, the BG2 fixpack, and possibly a few others,) then any content mods, then any GUI mods, then finally the widescreen mod.
I had a similar issue to you when I recently reinstalled BGT with other mods. In my case, the console not only read something along the lines of "Weidu version xxxxxxx", but also showed a hierarchy of previous installed mods, with a particular focus on one mod in particular.
If it's the same situation for you, then find the setup executable for that specified mod (in my case it was "Setup-GUI.exe", which is included with the BGT install,) start that executable, but
don't continue. Just quit and try again to install BGT. It should be enough just to start the executable to fix the installation order.
As I said, install BGT
before anything else (except BG2 fixpack and Ascension,) because otherwise, you really shouldn't be getting this issue.
Contact me if you need some more help or clarification. I'm no expert, by I spent days configuring the wineskin wrapper and mods to get everything working fine.
P.S.
Some more advice, don't use the special Mac installer for BGT. I just remembered that it has a different installation process that I consider to be more complicated than simply using the windows version. Download the windows version of BGT and use that. If you don't know how to run a setup executable with wineskin, just ask me for help.