Hi
The results of the 2d to 3d anaglyphs produce pseudo 3d and don't work very well (if at all IMHO) See my post to determine how you can get reasonable 3d with VP.
http://nch.invisionz...glyph-creation/
For correct 3d you require two proper L-R images (clips) each taken simultaneously from positions at least 2-3" apart. More for some effects.
These images can be colour or B/W.
Try these two... from a stereo card series I have on Egypt.
RIGHT

LEFT

You should be able to copy/paste these into VP.
This is a frame from an anaglyph .avi created in VP...

This is using the method I outlined in my post and doesn't use any of the 3d export options. The method works in colour just the same and also with L/R videos.
In fact I am not sure how one views the side by side or the one above the other images/clips . You can use auto stereo vewing in some cases possibly....perhaps someone can clarify this point.
Since my post on the subject and following tests with still images, despite VP not being able to merge tracks by addition, I have succesfully made some short red/cyan anaglyph clips with two video cameras fixed side by side.
Nat