Turns out somehow the function calls needed to grab data from the NI boards has changed. I don't know if there was an update to Image acqusistion toolbox or to NI vision software but now I need the following code to get data to be captured into matlab
vid = videoinput('ni', 1, 'NICFGen_Port0');
src = getselectedsource(vid);
vid.FramesPerTrigger = 30;
start(vid);
temp = getdata(vid);
stop(vid);
delete(vid)