I am unable to reproduce your problem. I can read as few as 4 samples from a single channel and still receive valid data every time (I stopped after 1,000 successful and consecutive reads). My setup is: RHEL 4, NI-DAQmx Base 3.4, USB-6211 (which is Dev2), function generator for external clock, 100Hz - 50kHz TTL square wave. Try using my code below, which is modified from acquireNScans-ExtClk.c.
Principal Software Engineer :: Configuration Based Software Senior Software Engineer :: Multifunction Instruments Applications Group (until May 2018) Software Engineer :: Measurements RLP Group (until Mar 2014) Applications Engineer :: High Speed Product Group (until Sep 2008)