Hmm...it didn't take an hour. It takes about 20-30 minutes, though. And this is on a total of ~225GB (80GB and 160GB).

I didn't fail any syncs.
I'm pretty sure it built the drives. It took a while and everything seemed to check out in hyperterminal.
I definitely didn't add any other software. I only ran the builder and the 2.01 for large disks.

The other reason I saw was drive problems. That's not out of the question, but the drives are practically brand new (no more than about 6 months).