If two images you've imported into Didger aren't lining up, it is likely that the two images are calibrated or georeferenced slightly differently. It could be that one was simply calibrated differently than the other (using a different projection, projection setting, or datum), or maybe one was calibrated incorrectly or not very precisely. If you calibrated one (or both) of the images in a raster project in Didger 3, be sure you warp the image (Image | Warp Image) before exporting it to a GeoTIFF.
You can open each image up by itself in a raster project and confirm that the calibration settings are exactly same for both images. If they are, note the coordinates of a common point on both bitmaps. If the coordinates are not the same, then the images aren't going to line up when you import them both into a vector project. You might need to recalibrate one to match the other.
Updated October 20, 2016