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John,
I can't find a Patrick Shannon in the NPSS&S system. In fact, the only Shannon in a Missouri unit on either side with the first initial "P" is this man:
No. Soldier Name Side Function Regiment Name
1
Shannon, Porter
Confederate
Cavalry
3rd Regiment, Missouri Cavalry
However, the Missouri State Archives show three listings for a Patrick Shannon. These could all be the same man, two men, or, less likely, three different individuals. From the information you furnished, I would guess that you have already seen that data. If he was, in fact, the Captain shown as being in Co. C of the 77th Enrolled Missouri Militia, that unit was in reserve during the Battle of Westport according to this site:
http://www.geocities.com/CollegePark/Quad/6460/CW/EMM/EMMr.html
Concerning men serving on both sides of the war: Yes, it happened more often than many realize. Sometimes, due to a lack of conviction in the cause, or fear, or both, men were reluctant to join with their more belligerent neighbors during the earlier period of the war when virtually all were volunteers. Once drafts were instituted on both sides, men may have been pressed into service by the side they had the least patriotic connection to. Many of these changed sides when the opportunity availed itself. (Allowing oneself to be captured when escape was easily had, slipping across lines at night, making their way behind the lines of the enemy while on furlough, etc.)
Since the population of Missouri was so divided, it is not hard to imagine that more men from this state might have reason to switch sides than from some other areas. Since he later served as mayor (I assume you meant 1865-66 instead of 1855-56), it is evident that Shannon had a political bent. He may have been one particularly atuned to the fickle winds of war, and aligned himself as he saw fit according to whomever he thought had the best chance of controlling his state when it was all over.
Finally, if this is really him, the fact that his rank as a Confederate is listed as Major, and that it would be highly unusual for there to be no record of a man with a rank that high in regular Confederate service, that rank may have been given to him as the leader of some type of guerrilla or home guard unit. I doubt very seriously that he was ever recognized as such by the Confederate War Department.
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