The Treasury seal was changed on our currency beginning with Series 1969 notes. At that point, FRNs were the only currency being printed, since printing of Silver Certificates and United States Notes had ended a few years before.

The Treasury Seal has also appeared in a larger format, and in different colors. Check out any of the pre-1928 "horse blanket" US currency, and you will see the Treasury Seal surrounded by a series of engraved arcs. Go back further, and you will see Treasury Seals in even larger formats -- for example, I have a piece of Civil War-vintage "Fractional Currency" in which a silver dollar cannot cover the image of the Treasury Seal.

As for the changes in the flag, quite a few governmental flags have changed over the years. The 1915 SecTreas flag likely has to do with the fact that, for many years, the U.S. Coast Guard was part of the Treasury Department.