I started a new IA run on bg2ee 2.6.6 recently, here are two incompatibilities found so far: Sassar is missing after the first dialogue with him; stronghold quests won't start for PC with a different class.

Here's another thread back when 2.6 has just come out: http://forums.blackwyrmlair.net/index.php?showtopic=5487

I doubt I will be able to provide meaningful help if you encounter something that is more critical, sorry. But I'll use bug reports whenever I actually get to updating the mod for 2.6.x