I suspect the pads are not correctly toed-in. This problem will not correct itself over time.
If the pads are parallel to the rim then when you brake the leading edge of the pad bunches up a little and bounces off the rim. Fast. So you get squealing.
To avoid this you should adjust the pads so that the trailing edge is very slightly closer to the rim. Most packaged brake pads have this explained on the package, and conveniently the thickness of a bit of cardboard is a good distance to have the leading edge out from the rim. So the instructions usually say "use the package as a pad".
The easy way is to put something under the leading edge of the pad, squeeze the brake lever slightly, then do up the mounting bolts slightly. Hold the brake pad with one hand (to stop it rotating), the spanner or allen key in your other hand, and the brake lever with your gripping hand. If you're disadvantaged in the hand department I find that doing up the brake pad lightly while holding the brake lever, then releasing the lever and holding the pad to tighten it works.
The Park Tool website has an extended description.