Which PXI controller do you have?
Are you targetted to the running RT executable when you power off your PC? I have never tried this, but it might have a negative impact. What happens if you switch execution target to LabVIEW for Windows and then close LabVIEW and shut down the Windows computer normally? Is this what you were already doing?
Also, does the startup executable communicate with the host computer in any way (TCP/IP, DataSocket, etc)?
What indication do you have that your RT application stops running?
Aside from these things, the only thing I could think of would be if your Windows PC and PXI chassis were on the same power strip and you were using the power strip to turn off power to the Windows PC. I doubt this would be the case, but sometim
es that which goes unasked can be the culprit, so I at least thought I'd mention it as a possibility.