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Go to Setup->Load... and load the setup named General_Freq. and Time Response. Go to Measurement->Settings… and select 4 ch. in the upper right corner as shown below.
In step 5 select the sampling frequency you wish to use, e.g. as shown below.
Go to Measurement->System Delay... to open the dialog box shown below.
In this dialog you can select any of the choices above since
we only want to measure the delay between the channels. Click the 
button in the dialog box shown
above if you like more information about measuring the system delay.
Go to Measurement->Sound Card... to open the dialog box shown below.
Press the 
button to assign the input channels as shown in the figure
below.
Now perform several measurements and compare the impulse responses of channel 1 and channel 2. If they are exactly on top of each other, then the input channels are sample-synchronous.
The figure below shows output channel 1 connected to input channel 1 and output 2 connected to channel 2, which means the same stereo pair.
This confirms that the input channels 1 and 2 are sample-synchronous, which would be expected.
The next figure shows output channel 1 connected to input channel 1 and output 2 connected to channel 3, which means across two different stereo pairs.
This shows a 1 sample time difference between input channel 1 and 3. This means that these channels are not sample-synchronous.
If the sound device has more than 4 inputs, you can control the other by switching channels in the multi-channel input device setup. In the figure below we have selected stereo pair 5/6 to be measured in Ch. 3-4.
In this way you can control that all available stereo pairs are sample-synchronous.
The figure below shows channel 1 versus channel 5 (ch. 3):
The next figure shows channel 3 versus channel 5:
If they are not sample synchronous but the difference is stable (e.g. always one sample), this difference may be corrected as a post-processing. It depends on what application you are using it for.
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