Like assembly, mosaic balancing is normally automatic and painless. You may sometimes have problems if the image is very large, or needs dramatic corrections:
The automatic balancer uses the history to work out how you built your mosaic. The balancer knows about left-right and top-bottom joins, but nothing else! If the history has other stuff recorded in there, you’ll see unhelpful error messages like unable to open tmp/xxx.v, or more than one root.
If you need to perform corrections to any of your sub-images, do them, save the image, load it again, and then build the mosaic. This will make sure the history of the image you are trying to balance only contains mosaic operations.
The solution (as with mosaic assembly) is to assemble and balance your mosaic in smaller pieces.
Suppose your lighting and camera set-up always produces images which are brighter on the right than the left, and suppose, due to some problem with your grey-card correction, this effect is not completely removed. You will find that when you balance a mosaic, the small differences between left and right edges of your sub-images will have been smoothed out, but they will have caused a large difference in brightness between the extreme left edge of your final image and the extreme right.
nip2 includes several functions which can help to fix this problem, the most commonly used being: Tasks / Mosaic / Tilt Brightness / Left to Right and Tasks / Mosaic / Tilt Brightness / Top to Bottom.