This is because the agent you talked with the second time rebooked both passengers into a new PNR. I am sure that the new confirmation number/record locator number/whatever you want to call it was different than either of the first two confirmation numbers. Just as it is not possible to combine two separate PNR's into one, it is not possible to increase the number of passengers traveling in any single PNR.
I hope the agent explained to you that he or she was reissuing the tickets on a single PNR. If you were not aware of this, you could have an ugly surprise when an expected upgrade did not clear at the window.