Hi Dave,
ALWAYS glad when you chime in on subject!
Some of the Muskets in the collection of Colonial Williamsburg came directly from Flixton Hall in Suffolk, UK when they were purchased in the 1950's. They are as close to "factory new" as we probably will ever see, because they were mounted on the walls as military trophies shortly after they were made and hung there for around 200 years. I am going to ask Eric Goldstein the next time I see him, what the finish was on those muskets is. There is little doubt in my mind they were finished in some kind of varnish.
Captain/Major Cuthbertson served in the British 5th Regiment during the Seven Years/French and Indian War on the Continent. They were involved in a raid on Cherbourg, France and some battles in Hanover in the Germanic States near the end of the War. At the close of the war, they went into Peace Time Garrison in Ireland. Cuthbertson's Treatise was published for the first time in 1768, just a few years after they were back in Peace Time Garrison in Ireland.
Since Cuthbertson's Regiment served on the Continent, they received the best Arms that British Ordnance had. This meant they had Steel Rammer Muskets and his advice about carefully inspecting New Arms, including the advice to very carefully inspect those Steel Rammers prior to accepting the Arms, comes in no little part from the fact there was a large problem with some to many Steel Rammers not having been hardened and tempered correctly. (Sorry about going off on a bit of a tangent, but just couldn't pass up the chance to note this.
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Not only do I agree with Dave that Regimental Artificers/Armorers could have used tinted varnish to make the muskets stocks more of one uniform colour; I think it important to note the Colonel commanding each Regiment would have ordered how the stocks were to be stained and
further finished after they received them from British Ordnance, but also each Colonel paid for it out of the Regimental funds or his personal funds. IOW, it was up to the Regimental Commanders and not British Ordnance. So that leaves open the possibility some stocks were or were not stained after the Regiments received them, but Regimental Artificers/Armorers would have been tasked in "laying on a coat of varnish"when needed, on active service. Varnishes "cooked up" by the Regimental Artificers "in the field" probably were of a bit different colour than the varnish used by British Ordnance when the Arms were initially "stocked up" or assembled. That would explain other colour differences.
Gus