I just want to add a few helpful pointers to this thread, as I assume there are leagues that will be holding their auctions this week. We did ours today using the MFL interface, and encountered many of the same problems that others in this thread experienced. If I could do it again, here is what I would tell my league:
1) You must have a player selected and a dollar value entered into the nomination box in order to get the nomination to work correctly: this was a consistent issue for us. If I recall correctly, the default $1 nomination bid is automatically typed in the box at the outset of the auction. However, because of errors and problems, everybody in the league refreshed the window several times, and the pre-typed $1 disappeared for some. Make sure they type that in before hitting nominate. Conversely, we had two owners manage to nominate a bid for nobody that counted against their salary cap. In other words, they won a player named "0000" for $1. I don't know if this was due to their failure to highlight a player when nominating or just a bug in the system. Fortunately, this is easily fixed. As commissioner, just pause the auction and click on the "delete auctions" button. This will allow you to view the list of sold players. You will need to delete the player named "0000" and then have everyone refresh their browsers.
2) The interface does not allow for errant button presses. We had some issues where owners hit the nominate button out of turn. Make sure everybody understands that this can bring the auction to a frightening halt. In general, people need to be aware that this isn't yet an interface like Yahoo or ESPN. Acting out of turn can really screw things up. And if you have to pause the auction, make sure NOBODY hits nominate during the break.
3) The "skip" button is important. As commissioner, you will almost certainly need it at some point. Because it just cycles through the different owners, each person skipped will be told they're on the clock as it cycles around. Make sure everybody is following the chat feature and tell them you're skipping around back to OWNER X beforehand. Otherwise you run the risk of getting even more screwed up, as somebody is mistakenly told they're on the clock as you cycle through the entire group to get back to the skipped owner. If they get a bid in before you skip to the next person, you'll have to wait for that auction to end before pausing, deleting, and skipping again. Be aware that there is a frustrating lag associated with the skip. I had to cycle through a few times in order to land on the right owner.
4) The EMERGENCY auction help button at the top is your friend. While it appears you're just filling out the usual MFL help ticket (response within 24 hours), we had a tech support guy in our auction chatroom within minutes. He solved a serious problem for us. Additionally, you should let your league know that customer support posts under the COMMISSIONER handle in the chat room. People were confused, thinking that I was typing the questions he was typing. This led to even more problems, as everybody in the league started responding. Let them know in advance that if tech support shows up, STOP POSTING. It was a nightmare trying to explain the situation to everybody in the chat room.
I like MFL a lot and have used them for years. They have correctly labelled their auction room as a BETA, as that is what it is. Based on their history, I am confident that next year's interface will be on par with ESPN, Yahoo, and the old fantasyauctioneer.com site.