There are three varieties of these Clerk Markings. The generally accepted belief is that their function was to insure that the registered letter was properly sealed, hence the marking(s) on the backflap showing that the clerk had looked there.
The first variety consist of very large letters like the example below. These are known only for "B", "C", "D", and "U". These were used between 1882-1883. The assumption is that there were only four clerks at this time.

The second variety is the one shown by the original poster. These are known only with letters "B", "C", "D", and "O", "S", and "U". These are found used between 1883 and January 1902. Those from 1900, 1901 and 1902 have the date in four digits, like the example here.

The third variety was introduced in 1900, and is known only with letters "E", "H", and "L". The letters are in a larger circle, and are very thin strokes.

The majority of registered covers sent from or to New York City will have these markings, but there are exceptions. There are no recently published articles about these markings that I am aware of.
Mike