If you are saving in fits you could process each colour channel in images plus and then combine them in astraimage or even photoshop. Alternatively you could try to stack each image in Registax and try its rotation function(never been that successful though). An alternative and this is probably the best bet if you want to buy the program and that is Registar. It's touted to be the best image registration and stacking prog around. Do each channel and then combine in Astra Image or in Photoshop.
See, heaps of choices
