I would suggest making your program a service in Windows 2000. Microsoft sells the WIndows 2000 Resource kit which has some utilities to convert any executable to a service. I think there are some shareware utilities as well. Then, make sure your service has a taskbar interface (a cute little icon in the taskbar next to the clock). This may have to be done with some external programming, but I am not sure on this. You will also need to make sure that the NI-DAQ service starts before your service. I think this can be done with some registry edits.
If you get this finished and working well, please post back how you did it so that we can share this knowledge with other users of LabVIEW.
Randy Hoskin
Applications Engineer
National Instruments
http://www.ni.com/ask