Program fault corrected only by complete shut down

What doesn't get shut down with a Restart that does get shut down with Shut down?

I am running a data collection software called QuickDAQ connected by USB to a DT9818 board. When the Run icon is clicked, the program enters a wait state; data collection starts when a trigger condition occurs. If the trigger does not occur, I click stop and after about 20 seconds everything appears to go back to the conditions that existed before I clicked Run. But when I exit the program and then try to load the program again, it will not reload properly. (It loads showing no connection to the data collection board, no settings, etc.) I have found only one way to get this restarted. I use the Shut down command to shut down the computer and then start it again (restart does not clear the problem). I can then load the program, but the settings for the data collection channels return to the default values and have to be reset.

I THINK there is a clue to what is happening in the observaton that a system restart DOES NOT clear the problem. Only a complete shut down and start will allow me to get the program loaded again. Does anyone know what restart might not reset that a shut down does?

I have watched Task Manager Processes and see that QuickDAQ.exe does not disappear when I exit the program after this missed trigger. When it runs normally I see that QuickDAQ.exe does disappear from the Processes window. (In both cases it disappears from the Applications window.) I have tried Ending it from Task Manager, but cannot get it to End. If I do a Restart, it does not reappear in the Processes window, but still can't get the program to load correctly.

I have tried using the "Safely Remove Hardware and Eject Media" icon to disconnect the data collection board after closing the program following a missed trigger. However, the message is that there is a program still accessing the board. Since the trigger signal comes from the board, I suspect that there is some subprogram waiting for that trigger that doesn't clear when the program is closed. I have also tried unpluggin the USB without using the icon, plugging it back in and then trying to load the program; still no success.

I have worked with Data Translation (makers of the software and DT9818 hardware); they have been unable to duplicate the problem.

If I knew what the difference was between Restart and a Shut down and start, perhaps I could figure out what is causing the program to fail to close completely.

If you know someone who might know the answer, please bring this to their attention.

A completed shutdown clears the memory and removes the power to most everything. Their for when you do a cold boot the bios go through their check and Windows go through it checks and things are set back to where their suppose to be. One my two Windows 7 PC's I notice that on a restart the motherboard, fans, video card and fan still run. A cold start up can solve many small problems also. At times it helps Windows Up Dates install better than a restart.