I've had this happen several times to both OEM and aftermarket rotors and pads.
It's got to do with how evenly, or unevenly, pad material builds up on the rotor. Even the slightest variance will cause a vibration upon initial application of light braking at speed.
I get the vibration after going through a carwash. The spray of water seems to dislodge a bit of the pad material from the hot rotors. Sometimes rebedding will smooth it out for a while, sometimes it won't.
If the vibration doesn't go away, you could try taking the rotors off and lightly sanding them with a 220 (?) grit sanding media (check with the Stop-tech white-paper for the correct media) to take off the existing pad material and then go and rebed.