I had a pair of Duets in my old media center, and they were real stinkers with Windows Media Center. I would often get the same message the OP has gotten. Plus sometimes the cards would cause Media Center to abort a recording, and nothing would record until I rebooted. I switched over to SageTV, and it seemed to be able to handle card failures better, but I would still get multi-part recordings every once in awhile.
I built a new media center this month and went to a SiliconDust HDHR and ArgusTV for recordings. It's been basically rock solid.