Make sure that you are using the Check Reference function after starting the Find Reference move, before tyring to load a different velocity or acceleration. These errors look like the controller is still in the middle of finding the reference, when another move command or load command is issued.
Try running one of the example programs that ship with the Motion driver to see if you get the same error, which are located in the folder C:\Program Files\National Instruments\NI-Motion\FlexMotion\Examples\C\Find Reference (if you are using C programming - there is also a VB folder).
Hope this helps-
Julie S.