I would say either its the brakes wearing in on the old discs or you have a piece of meta rubbing somewhere??? Possibly a brake pad wear sensor???
I cant see how a groove in the pad cause a squeak - its just you have slightly less friction area.
If you have checked everything else then Im leaning towards pads wearing into the old discs as ive had a similar noise from mine in similar circumstances. Its annoying but it will fade away.
What does everyone else think?