BG2 fixpack is totally incompatible with Improved Anvil.
I don't recommend the G3's BG2 fixpack even to players who don't play Improved Anvil.
Main Reasons:
1- G3's BG2 fixpack is a heavily bugged mod itself which adds more bugs to your game than it fixes. It has fundamental methodological problems which keeps it bugged. Releasing hotfixes and new versions won't solve its problems; so, it's not even a question of which version you want to use.
2- Many of the changes G3's BG2 fixpack applies to the game are not "fixes". They are rather arbitrary and unwelcome changes and tweaks under fixing disguise.
Known incompatibility inssues with Improved Anvil (there may be more which have not been detected yet):
- The BG2 fixpack's (and Oversight mod's) changes to creatures' alignments will break clerics' scripts in Improved Anvil.
- Bg2 fixpack has arbitrarily changed Tolgerias's death variable. This can break one of the scripting blocks during that particular battle.
- Bg2 fixpack has arbitrarily changed/increased some of the original game weapons' enchantment levels (for example, it changes Daystar to a +4 weapon!); those weapons' enchantment levels were correct in the original game and no change was needed for them. One can ask why should a mod which claims to be a fixpack play the role of an Item-Upgrade mod. Apart from the illogical and arbitrary nature of such changes, they affect the desired difficulty level of some of the battles in the game in an unpleasant way.
- BG2 fixpack has made arbitrary changes to some of the game's files (spells, creatures, etc) which can cause problems during some of the battles.