Sounds like you might not have enough interchannel delay so the second channel doesn't have time to settle. The AI Config.vi routine has an input for specifying the amount of delay to insert between reading channels on a scan. The default value is a -1 which tells LV to figure it out on its own--sometimes this value is too short.
To see what LV is selecting, there's a subVI inside AI config called AI Clock Config that outputs the value LV selected. Probing that point while your code is running will give you a starting place for adjusting the interchannel delay.
Mike...
