Bill,
I'm not that familiar with TDS3000 scopes, but I did notice one thing in what you said that you might want to look in to.
You want to capture 'the entire scope "face" or from the trigger to right side of the scope face'. The trigger is not necessarily the left-most value on the scope display. All modern digital scopes have a pre-trigger feature that allows you to collect points before and up to the trigger as well as after the trigger. If half of your scan consists of pre-trigger points and you somehow ask the scope for data from the trigger to the end of the scan, you might see the behavior you indicate.
Just a shot in the dark. I hope it helps.
TonyH
Measurement Studio