Juan,
Still doing this, but I have noticed a pattern. If I debayer from one external drive to another I'm almost (note the almost) guaranteed a crash. However, if I shunt the files to the second hard drive before running debayer then there is no problem. So, this probably has something to do with the USB system in Windows. Note also that the target drive also hosts my temp folder.
Cheers (and a Merry Christmas),
David