There was a small incompatibility in the mod relating to the 100% spell learning mod which stopped it installing for the GOG version.

I emailed the author with the details and he sent me a quick fix and promised a new version will be out next week but I thought I'd let everyone here get it a bit early

"Overwrite setup-iwd2tweaks.tp2 in your iwd2tweaks folder with the attached version. I'll publish a fixed version next week."

To be specific, the error isn't related to the gog.com version of IWD2 - it's a straight programming error on my part that would prevent correct installation even in the CD (or DVD) version of IWD2.