After I was getting bored I figured it was time for a Baldur's Gate playthrough from start to finish.
I loaded up BGEE and wanted to use an old kit I had laying around (Morituri).
Updated the kit and proceeded to play through the game.
Now I'm ready for BG2EE, installed the kit and imported my character from the BGEE "final save".
Aaaaaand I'm a Grizzly bear.
I had to read the kit description twice before realizing I was indeed reading it correctly.
I wondered if the mod simply wasnt working with BG2EE and started a new game.
My custom kit works fine with a new game.
Importing a BGEE savegame that was using my custom kit however will proceed to generate a character with the "grizzly bear" kit in BG2EE.
While I can probably fix this using an editor, I want to try and fix the mod so this doesn't happen in the future.
Hopefully someone else has already come across this?