if every third shot is landing right where the sun is, that might be your problem.
as it is throwing your exposure off.
you need to use the same exposure and lock it for all the shots.
1.for the sun, try to cut the sun in have with the edge of your lens on the first shot.
2set your exposure and lock them.
3take the first shot
4then do the rest of the shots.
Hi Ray,
Having looked at this panorama it is clear that the positioning of the sun is centered to the lens and this is never a good idea. Also the camera needs to be set up in manual mode as to lock the settings to make 100% sure all the images are shot with the exact exposure etc. This also involves manually setting the white balance.
To extract the most from this set up it is recommended that you shoot in RAW mode and learn to process these RAW images to there best advantage. Doing this allows for the reduction in Chromatic Aberration and Vignetting and when done in a batched way assures you that all images are processed the same way. (Unlike allowing the camera to .jpg process them)
Regards, Smooth 
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