It's possible that the old rotor had some degree of disc thickness variation and runout prior to installing the new pads. So, I guess when you add normal wear to that, it eventually reached a point where you noticed problems.
This is why I always recommend either resurfacing or replacing the rotors with every brake job. The rotor may be near the specified limit for runout or disc thickness variation (but is still okay at the time of the brake job), but shortly afterwards, problems will arise.
Replacing or resurfacing the rotors will resolve the problem. If you do the work yourself and can have the rotors resurfaced for under $15/rotor, I would give that a try first.