Hi Ryan,
I believe you need a cleaner clock source at the connection to the DAQ board. My suspicion is that you are experiencing reflections and transmission line effects. To help these noise issues, it is advisable to try and use the shortest length of wire possible to the 6534 board and to twist a grounded wire around your clock signal. This will help attenuate outside interference.
I've included a note describing these effects in more detail. Another option is to sample your clock on the falling edge. This is really only a consideration on data input though. Anyway, hope that helps. Have a good day.
Ron