John and Kirby,
While looking for something else today, I happened upon my 2002 and 2003 emails with Jim McGhee and Jim Thoma regarding this issue of the hidden gunpowder, and also found references such as a copy of the McNamara memoir written about 1865 and other things.

Jim Thoma, who wrote the Cooper County in the Civil War history called "This Cruel Unnatural War" in 2003 and published it himself from his Kingsport TN home, replied to my inquiry about this issue with detailed information. Thoma said Captain Joseph Kelly of the "Washington Blues" left Camp Jackson in April 1861 with his two companies of Missouri State Guard troops as well as Captain Robert McCullough and his five companies, and had a harrowing trip escorting the gunpowder from St. Louis to Jefferson City aboard the "Isabella" and the "Augustus McDowell" river packets. Thoma wrote that the a fierce spring thunder storm demoralized the regular crews of the two vessels, who deserted their boats somewhere enroute fearing frequent lightning would set off the powder. In his memoir, MSG Captain Ai Edgar Asbury, who headed a group taking three wagons, south from Jeff City about this time, also wrote about his very real fear that leaking kegs of powder would ignite and blow up the three wagons and drivers that he commanded.The MSG troops had to load the gunpowder aboard themselves at St. Louis, and also had to act as temporary crew. When they reached Jefferson City, Governor Jackson greeted these tired MSG men, and may have arranged local convicts to offload the gunpowder.

Thoma maintained that Captain Joseph Kelly of the Washington Blues," probably commanded the MSG escort bringing the powder to Jefferson City, but that he was otherwise busy with other duties during June 12-16 when unknown parties removed the powder from Jefferson City and distributed it all over the countryside. Thoma pointed out that Captain Kelly led the MSG contingent that burned the two Pacific Railroad bridges over the Osage and Gasconade Rivers and did other things between Jun 12 and June 16, in a vain effort to slow down the Union advance. Therefore, the captain himself did not spririt away the gunpowder that he personally supervised bringing to Jeff City on the two named riverboats.

Jim Thoma maintained that Captain McCullough and his men and their overall commander, MSG General John Sappington Marmaduke, probably took the gunpowder and distributed it up the Missouri River, and all over the place. Jim Thoma made a convincing argument based on careful analysis of the remaining facts. Whomever distributed the stuff did a thorough job, because Union troops hunted for the powder over the next four years, and found a number of the hidden caches of the stuff, as written in several sources.

Bruce Nichols