japflare,
Thanks for the question. The issue as you describe it is not one I am familiar with (it hasn't been reported as a major issue in the past). I have, however, seen enough issues that cause "similar" problems to make me think of this being a software (driver) issue. Once you have configured your SCXI devices in Measurement and Automation Explorer (MAX), you should not have to go back in and reconfigure accessories. You also should not have to reset the device every time you restart the computer (devices should be setup automatically at the startup). Basically, there isn't anything in that you could do in LabVIEW that should cause this issue.
If you still have your driver CDs (NI-DAQ, NI-VISA, NI-SWITCH, NI-DMM, etc) then you might want to try and "repair" your installs from add/remove programs first. With the symptoms you are describing, the problem most likely is with NI-DAQ and/or Measurement and Automation Explorer. NI-DAQ and MAX are responsible for installing all devices and configuring them with the OS. If a repair does not seem to work, you can try uninstalling and reinstalling all of your hardware drivers (you can leave LabVIEW alone). Checking your driver installs is really the only way to get around the issue since this isn't a matter of something you are doing wrong. If you are still having problems, let me know what errors you get in LabVIEW if you don't reset in MAX first. I hope this helps.
Best Regards,
Jeremy R.
NI - Applications Engineer