Your first program is really the way you want to go. To prevent glitches in a continuous acquisition you certainly only want to do the Configure, Start, and clear outside of the loop. To prevent problems in this configuration you can tweak a couple things. First, the buffer size doesn't have to be as large as your entire acquisition - in fact it doesn't need to be anywhere near that large. Usually 2 to 3 times the amount of samples you are reading at a time should be sufficient. Second, you can alter the amount of samples to read at a time in the loop. The larger the number, the less overhead there is since you are grabbing larger chunks from the buffer at a time.
If you continue to have problems with the original program, just post back. Also, in the futur
e, I would recommend posting to the LabVIEW or DAQ group rather than DSC - you'll get a lot more and quicker responses that way.