Hi Burr, sorry no I didn't understand correctly. So it sounds like you're talking about this kind of display artifact discussed here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=4987.2

A 3D perspective viewport has a little different kind of depth behavior than a 2D one, so it's not too surprising that you would see slightly different behavior with depth sensitive operations between them.

I do have some ideas that I'd like to try to experiment with for reducing that type of display artifact in the future.

- Michael