Gaurav,
This behavior you are experiencing is a result of a combination of factors. 1) The 6008/9 has a very small onboard FIFO. 2) NI-DAQmx Base is a driver written in the user level. 3) Communication with the device is message based over USB which is inherently slower than equivalent communication over PCI. Since NI-DAQmx Base is written in LabVIEW, it has user level priority and CPU allocation. If the operating system is busy with other user level operations, NI-DAQmx Base can get starved of resources so that it cannot request data from the USB device fast enough. Since the USB-6008/9 has a relatively small onboard FIFO, it does not take long for the FIFO to overflow if you are acquiring at a high rate. Unfortunately, the operations you mentioned (e.g. opening other programs, minimizing/maximizing windows) are very CPU intensive, especially with Windows OS. Therefore, when you perform these operations, NI-DAQmx Base cannot retrieve data from the device, the FIFO overflows, and you get the -200361 error. The best solution, currently, is to minimize all other operations on the computer in order to prevent this potential starvation of NI-DAQmx Base. We are investigating other solutions that may be available in future versions, including providing driver support in the kernel level to prevent this kind of resource starvation.