You're playing 3.5 while using the Book of Exalted Deeds. Balance isn't just being ignored, you pushed it out of a window on top of the Burj Khalifa.
Yeah, I see that now, along with several other books.
I started this campaign almost 2 years ago, after not playing dnd for like 15 years or so. I ran rolemaster for a while during that time, but hadn't roleplayed in a while before that point.
Going into the game, I was unfamiliar with the rules (still trying to get in all the reading and stuff). The only book I saw people having huge issues with as I started my research was Unearthed Arcana (which I banned) and allowed use of everything else. Because I felt that one of my strong suits as a DM/GM was to incorporate and include just about anything.
The biggest issue that has really crept up, is the the player in my group who is a VoP/Wildshape/Druid has been breaking/ignoring the rules since day one and it's been a struggle ever since. In the beginning I trusted the players to be on the up and up about stuff. And pretty much everyone was, but him. Either by ignorance or choice. We are all friends outside the game, so I am doing my best to work through things. The biggest problems I've had with him are stacking things that don't stack, staying in wildshape form in anti/dead magic zones, giving himself and his animal companion extra hit points and applying BAB additional attacks to his dire wolf companion.
Granted, I put a significant amount of the blame on myself. While my skills are pretty solid in setting up a story, world, ect... I've spent the past 18 months or so learning the rules as I go.
So, now I find myself questioning every little thing he does. And I am in the process of breaking down his character spell by spell, figuring out what his stats/abilities/numbers really are. Because the spreadsheet he set up has several flaws in it.