We got stuck at some point -- it wouldn't download at all. This got us going again:
http://www.innovationfirst.com/first...Action=Q&ID=73
Which says, in part:
"To force your 2004 EDU RC into Wait-for-Download Mode (PROGRAM STATE orange) you can hold down the PROG button while turning it on. You must release the ON/OFF button before releasing the PROG button."