This is interesting. My first reaction is to say that's a symptom of cable trouble or IDE header trouble, and that it's got nothing to do with the builder software.

Mark, can you confirm or deny the concept that the drive's position on the cable could affect the builder? Is there anything, even at the lowest level, that could cause that behavior he observed?

I can understand possibly needing to have only one disk drive plugged in for the builder to work. But having it need to be on a certain header? That just sounds like hardware/header/cable trouble to me.