I'm not sure if this is the problem, but it might have something to do with what you're seeing.
When you leave the machine running, does the computer go into "standby" mode? If so, this may be causing the problem. When a computer enters standby mode, power likely gets cut from the PCI bus, and will reset the DAQ board. Since NI-DAQ doesn't know the device has been reset, that will cause problems.
If your computer is configured to enter standby mode, I would suggest to reconfigure your computer to never enter standby mode.
I hope this helps.
Regards,
Todd D.
NI Applications Engineer