I ran into a weird issue recently as well. The commissioner threatened to remove my team because I didn't reject his trade offer on a timely basis (a week during the offseason and the Memorial Day weekend). There was some history here and we already had a long (what I thought was positive) e-mail thread with me telling him I wasn't interested in the players involved in the trade and my rationale, etc. After I went in and rejected the trade, he removed my team.
In our subsequent e-mail thread, it was clear we were not on the same page. E.g., during the draft, I made a trade for draft picks and the clock expired before I was able to make my pick, and replied to all complaining about the situation. He immediately got defensive and told me it wasn't his fault and later claimed I accused him of doing it on purpose. When I told him he was reading more into my e-mails than was actually there, he said he was "insulted that I would question his reading comprehension skills". He also pointed to the disagreement we had re: player values, strategy as evidence that "I thought he was stupid". He removed my team because I was "a negligent owner" and then when I got upset at him for doing so told me he was considering letting me back in until I was obnoxious (which as I said it was because I was being obnoxious.
The moral is that some commissioners let the power go to their head. It's "their" league, and God forbid if you question them. As I pointed out to the commish in the previous story (and which he took great offense to), there is an inherent conflict of interest when you are running the league and competing in the same league, especially when there's money involved. A commissioner needs to be able to separate his roles as an owner competing in the league and the administrative role in running the league. It's a very difficult thing to do, but if there's a situation that even LOOKS like there might be something amiss, it's important to remove all doubt. This is why I use an executive committee in the leagues I run, and excuse myself (and others) for any decisions where there is a vested interest on one side or another.