Hi Simon
There is a trick to speed up things when using DynamicAligment. Before canceling the first instance, create a new process icon with it. Then, when you have selected the reference and target images for the new instance, drag the process icon and drop it on the bottom bar on DA's window. This action will load all the samples that you used before. Of course many of the sample may be misplaced on the new image, so you'll have to manually check if they are on the right place, and move them if not (it is quite rare that the reference samples are misplaced). We'll work next year on some improvements for DA, thinking on these reusable samples, to realign them correctly.
Now, about your big problem. If your images are not too deep, and there are lots of free background sky, I suggest you to use AutomaticBackgroundExtractor. If there are only additive components, with it you may directly substract the model.
Other suggestion. When you finish processing all the images, open the AutoHistogram window. Disable the clipping option, and just enable the middtones balance. Now, bring your prefered image into focus, to act as reference frame, and click on the "As target" buttom. This will load the image's statistics to AutoHistograms, and set the midtones balance. Now, just apply this process to every other image (you may create a new ImageContainer to speed up the process). This should leave are your images with the same background tone, and is very likely that the other objects will look very similar. It is very important that you had set propperly the black and white points, there are no black lines or columns, and that you had been very carefull with color balance in your normal processing workflow (avoid using exotic curves).
I think that this should work...
