Hi Magnus,
Another way to try and 'align' the three channels (once extracted from your RGB image) is to use
Script | ImageAnalysis | ImageSolver (on your RGB image, or the L-channel extract thereof) to determine the optical characteristics of your OTA
Script | Render | CatalogStarGenerator to create a 'synthetic' reference frame against which you will then align the R, G and B planes
Process | DynamicAlignment on each of the three (R, G and B) channels, aligning these against the synthetic image you have acreated above
You can then recombine the R, G and B channels to see if you have improved things in any way.