The mystery:

W. H. Malkin Co. used this perforator—apparently around 1910:

These are the reported cancels:

The pattern is also reported on Scott No. 92 and 98, both of which were issued before 1910.

Starting in 1913, we see a new pattern:

Why was the original machine modified or replaced?

The solution:

Unsolved!

The perfins are very similar, suggesting that the pins for "Co" were removed. We know that the second pattern was a multi-headed machine—were there too many pins (55) in the original design for ease of use? By way of comparison, the International Harvester machines generally had:
  (5 dies) x (34 pins/die) = 170 pins

The WHM/Co pattern on a 5-die machine would have had:
  (5 dies) x (55 pins/die) = 275 pins

The WHM pattern on a 5-die machine would have had:
  (5 dies) x (42 pins/die) = 210 pins

Perhaps 275 pins required too much force to be easy to use.