I use a Sony RM-AV3000 for the rest of my gear so that's good to hear that it's not the unit itself, but the remote.
I'm assuming I just need to "learn" the sony - time to break out the manual again...
jmsaul, if you have specific information about learning remotes and the roku I'd love to hear it. If you can, post it here or email me a - hcraig at gmail d0t com.
I have a slightly-rearranged file for a new generation Pronto, but I don't think I can do much for you on another remote -- I could give you the Pronto hex code for Stop, but unless there's some way to translate it I don't think it would be very useful.
If you're in the area you're welcome to come by with your remote and learn it from the Pronto, though.
Roku also provided a number of other buttons that exist only in the Pronto file, for application developers to use. So far, nobody has. I believe these are IR commands that the HD1000 will respond to, but the stock remote doesn't have a button for.