Running FPGA and DAQmx on the same VI

I am using three cards on my computer: 2 PCIe-7841R and one PCIe-6361 and i am trying to control digital outputs, along with analog inputs and outputs on all cards from one VI. The controls for the R series cards works just fine, but the analog input for the PCIe-6361 is giving me unexpected voltages that are negative. If i try to control the PCIe-6361 on a separate VI it works just fine. Is there a way i can control all cards on one VI or is there some kind of conflict going on?