When we started woring with this we found the same problem. After investigating this, we found that the manual has a typographical error.

To make the elevons work properly you must set it up as follows:

Right-hand control surface in channel #2
Left-hand control surface in channel #1

This is the important point.

You then set the channel reverse setting to get them to work in the correct direction. Depending upon which side of the servo your pushrods come off, both channels will be set to normal or both to reverse.

This works whether the control horns are on the top or the bottom of the control surface.