Do you have the LabVIEW Sound and Vibration Toolset 3.0? If so, perform an acquisition and use the SVT Gain and Phase VI to measure the interchannel phase mismatch.
Using analysis available in the Full and Pro versions of LV you can perform a similar measurement using Extract Single Tone Information.vi found in the Analyze-->Waveform Measurements palette. Subtract the phase returned by each instance. The phase of either channel independently is irrelevant, but the relative phase should be accurate.
Doug
Enthusiast for LabVIEW, DAQmx, and Sound and Vibration