I wouldn't use the stacks from SharpCap, PixInsight has tools to select/discard bad frames and first class algorithms to align and integrate images, export the raw fit files and work from there, I believe the stacking facility in SharpCap is live stacking and only intended for viewing in a live situation, it was never intended to be used for processing images....but I may be wrong.
Have a look at Warren Kellers book on PixInsight it has suggested workflows, I wouldn't be without it!!