Hi John,
Until now I would have said that it sounds like you should be using
flip_texture=1 option in your CFG file. In the past, differences in the way that different texture formats store their data could cause a texture to appear flipped.
However, we've been cleaning up Cal3D a little recently and have made it so this will now be applied automatically when it is needed. This update will be in the next release, which should be going up on our
download page tomorrow (25 Feb, 2015). Be sure to grab both the Cal3D Exporter and new version of Vizard.
For now you can test this by vertically flipping your texture.