do a transfer of the same show over both the soundcards
then you will need to crop each show to start/end at the same bit, which is a little tricky but is fairly easily done
i use sf 6.0 and you can magnify it down to the bit, which will eventually be just dots to signify samples
i used a peak or a low mark in the recording so i could easily find the same sample in the other recording
once you have cropped them to start/end on the same samples... open eac and choose Tools > compare wavs. it will ask for the first and then second wavs to compare, then it does the rest and will tell you about droped samples and what not