[Stiglr]

That can certainly be, if the TCE assigns different faces to the same part of the graphic (overlapping); and, with all the faces of a cube being perfect squares, that's all too likely. Remember, if you start by just mapping to any one view, all the surfaces will be jumbled into a square and plopped onto the face of the graphic en masse... until you edit it otherwise.

What you'll want to do is:
1) Select only the faces for one side
2) Look at them in the TCE (and they will be the only ones shown in tinted green at that point)
3) Re-assign their view aspect.
4) Change something else; rotate the tinted square, resize it, flip it horizontally or vertically, move the square around the graphic, etc., and then observe the effect of each on the side in the AC3D viewports. Do this until you can visualize what the difference is between what texturing you have, and what texturing you want.
5) Move, rotate, scale or edit the surfaces in the TCE to get what you need. The TCE has the flexibility to move each VERTEX, if you want, in order to line up surfaces to the texture.