Tom, if it were my system I'd consider reinstalling the software AND having a dedicated PC to run the control. I don't have any experience running in dual-boot, but Win seems to sometimes have enough trouble running in single boot that I'm not about to get adventuresome.
I have a spare flash drive that has the Centroid OS/software installed on it for "just in case". I've had too many instances of my regular Win XP PC coming up with "warning Will Robinson, we are losing all your dataaaaaaaaaaa . . . ." to trust that things won't just go sour.
Perhaps your Win installation is dieing and is doing its best to take the Linux install down with it. It certainly sounds like the Linux OS is having trouble recognizing system components.
The Centroid/Ajax control doesn't need a super hi-zoot computer with kewl graphics card etc to run on, and if you look around it seems like you could find someone upgrading a 4 year old system that would let you have their old P5 system for a song. Giving your mill a dedicated computer would seem to be an easy way to go, just to reduce the possibility of inter-system conflicts.
It may well be that you do have hardware issues. A dedicated PC for the machine could help to pinpoint them if that is the case.