A few other people have also had this when running disks from something other than the onboard SATA controller.
One user fixed his by updating the firmware on his SAS card.
What I think is actually happening, is that the preclear script is detecting a different situation(or non-standard, or something it is not sure about), and asks for an 'extra' prompt before continuing.
It's very hard(maybe impossible) for gfjardim's wonderful GUI front end to catch this, and hence gets stuck at that point.
You have a couple ways around this:
Move the disk(s) to the onboard SATA to do the preclear.(and move it back when finished)
Run the script directly within a terminal session.(I believe you can still monitor progress from the GUI)
possibly, try any available firmware updates for your card
