So, I noticed something strange when I got a new C: HDD. I didn't bother reinstalling NWN:EE on Steam, I just reinstalled the Beamdog version. But, the toolset started crashing and all kinds of errors occured. I didn't get it, until I thought maybe it has something to do with not having the Steam version of the game.
Indeed, after I installed the Steam version, everyting has been fine, no crashes or errors.
Just something you might consider if the toolset keeps crashing. Install the Steam version too.