Are these issues still there if you download the RAW files and merge them manually (say in Lightroom)?
I believe these functions are quite processor intensive and maybe, I've seen a similar problem temporarily on the screen during a flight but I always just record RAW and merge manually. Maybe try smaller jpegs. When doing it manually you often get black segments in the corners just because the pano doesn't have images to cover the whole area. If auto is selected in Lightroom it just crops the black out. I prefer to load it into PS and use Fill/Content Aware to maintain the largest area if possible.
Nice view, no bison or deer?