In reply to due:
That's hard to answer without looking at your images.
Is the problem that it is failing to match overlapping areas of your images correctly, or that the orientation & projection of the results are wrong?
If it's the former then you can manually add control points to pairs of images. This is boring as hell, but never fails.
If it's the projection & orientation then the preview tool lets you tweak that, although it's a right pain in the backside to use.