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Why does my computer, running Windows 2000 and LabVIEW 6.0.2 plus GPIB ver. 1.66, reboot at random when running my application?

It seems to be an IRQ conflict ... especially if it's the PCI PnP one.
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Although I'm not sure what specifically is causing the problem, I can surmise that you're experiencing a 'feature' in Windows 2000/XP. By default in these OS's, if there is a major system crash the computer will automatically reboot. You can change this by right clicking My Computer->properties->advanced->start up and recovery and uncheck the 'Automatically Reboot' box.

Now when your system crashes you will likely see a classic Blue Screen of Death.
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