It might be a good idea to let the disk builder run two or three times consecutively.

There is a bug in it, and if that bug happens your partitions will not be corretly implemented. I had this happen to me EVERY time I used disk builder.

The easy fix is to let the disk builder run two or three times consecutively. (just reboot the empeg with the disk builder on it and press <return> once it's booted IIRC)
Sure, it takes a little while longer, but then you can be sure of a perfect install.

Hope this helps.