Zacharoo, I'm a Ruger "enthusiast" not a "collector" but I did find what might help in answering this question. In looking in the Third Revision of The Red Eagle News Exchange, Volume One, on page 47 where the .44 cal. Flattops are being discussed;
I quote, "Note: Sometime between s/n 24569 (shipped December 1960) and 26776 (shipped February 1961), the "S" proofmark found on the front of the .44 flattop cylinder was changed from 1/16" height to 1/8" height."
But since the .45 Blackhawks didn't show up 'til way later, this does not explain why you have .45 Colt cylinders with different size "S" proofmarks.
In reading further in RED concerning manufacture of the OM and NM .45 Blackhawks, there is no mention of different size "S" marks on the cylinders.
I have an OM .45 Blackhawk Convertible manufactured in 1971. Both cylinders are marked with the larger "S" proof mark. The cylinder on my OM .44 Blackhawk Flattop shipped in 1959 has the small, 1/16" "S" proof mark for whatever that's worth.