Yup, there is indeed a bug, but it's not related to drive size. Apparantly it can happen to any drive, the size doesn't matter.

Last week I tried it with a 30gig drive (hardly a big drive nowadays), and ran into the same problem.

The only thing I can think of is that the bug might not happen with a completely new drive, so one that doesn't have any partitions on it. But I am not entirely sure, I haven't tried this enough to be able to say this with any degree of certitude.

But you're right : the problem is indeed easily enough fixed by letting the builder run two or three times, but it's still very annoying. Especially if you've already re-flashed your Empeg with the 2.0 kernel and then have to re-reflash it with the disk builder to actually get things done...