If you order a BTO Mac Pro with two internal hard drives, you may want to make a note of this. To make a long story short: Before firing up a new Mac Pro configured with two internal hard drives to run the Migration Assistant, turn it on in Target Disk Mode and rename the empty second hard drive to something other than Macintosh HD. Now, the explanation:
I was setting up a new Mac Pro for a user at one of my clients, and attempted to migrate her from her existing Power Mac G5. The new machine was configured with two internal hard drives, 500GB each. I attempted to migrate her data from the initial Setup Assistant, and everything went smoothly until we got to the actual "Transferring Information" screen -- no time estimate ever appeared in the progress bar, and the drives were not making sounds that would indicate they were being accessed.
I ended up rebooting the new machine via the power button and choosing not to migrate data when the Setup Assistant ran the next time. I made a dummy account and then ran Migration Assistant manually. I noticed that both internal drives on the Mac Pro were named Macintosh HD, and guessed that may have confused Migration Assistant. After I renamed the second drive, the copy proceeded without any problems.
To verify that the identically-named internal drives were indeed the problem, I stopped the migration, set the machine back to out-of-box state (except for the internal drives having identical names), and tried migrating the data from the initial Setup Assistant, and it worked flawlessly. I submitted a bug report to Apple about this, but thought I'd spread the word to possibly save someone else some time figuring this out before it gets fixed by a future version of Migration Assistant.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20070807115154337