I am running the latest build, and I did partition the drive myself. I suppose it's possible that I screwed it up, but I did partition my first empeg the same way, and I'm very comfortaible that I did do it correctly. It's not very dificult to fdisk a drive and mkfs it, but then again, when it doesn't work, it doesn't work!
The thought did occur to me that I should probably just redo it using empeg's tool and that's probably what I'll end up doing. I can't think of anything else to try. Plus that way, the fsck flag will be reset so even if it doesn't really correct the problem, it will still give me a month or so before I'll have to worry about it again.