The two acquisitions should not interfere with one another because they use separate drivers. The bottleneck may be the PCI bus, but doesn't seem likely due to your slow acquisition speed.
Try running your VI without the DAQ portion, to make sure the ADC motion section is working the way you expect it should. If it is not, then it doesn't have anything to do with the DAQ, and you should try an example program to see if that works.
Regards-
Julie S
Applications Engineering
National Instruments