EducatedOaf

@EducatedOaf:
Did you check your baldur.ini files in both your BG1 and BG2 folder? There are parameters containing paths to the disc content. They need to match your current directories.
Personally, i found using exactly the same install folder as suggested by the installer working best, that is Baldur's Gate for BG1 and BGII - SoA for BG2.
Make also sure to fullfil the requirements (latest patches, create and save a game in EACH BG game) before starting a megamod install

@Rakhu

I'm using GOG, so no ini's. I've done it before this way, so don't know why I'd need ini's.

That wouldn't explain why it's asking for BG2 files for the BG1 directory.

I'm going to try it from the download, clicking the no update shortcut. - That works, but is outdated.

This would seem to indicate that the latest version on git is bugged.

Using the latest update of BWS.

When I select the directories for BG1/BG2 I get an error telling me that my install is incomplete.

For BG1:

Determining spells and script for RIBALD
This is Stratagems Scripting Language

 
 Input file is stratagems/mage/ssl/bg2/main/dw#fgmag.ssl 

 Output file is stratagems_external\workspace\ssl_out/dw#fgmag.baf 

Failed to patch RIBALD.CRE; error message was Out of memory

Failed to patch RIBALD.CRE; error message was Out of memory

I'm going to try to narrow down the SCS bug over the next few by systematically ruling out mods, installing many many times.