OK, as the wait is only 1mS and the sample rate is 20mS and there is no dataflow between the aquire vi and the wait(ms) the wait will not have an affect on the timing. Unless the sound input dll is somehow blocking, but i doubt that. If you post the actual VI (in LV2011/12) I will run it and see what happens. I also suggest you put a tick count (ms) in the top loop and look at the itteration timing, this may help to identify the cause of the glitch.
Michael