There are different quality of replacement rotors out there. Some are junk and some have better metallurgy etc. as well as junk $8 pads. Most pro mechanics I know will only mess with the top shelf stuff and turn brand new rotors out of the box before installation. One problem I have run into multiple times is that not all bearings and races are created equally. I have seen size differences in the roller diameters, roller widths and the way the rollers sit on the races between Koyo, SKS, and Timkins so I always knock whatever generic unknown races out the rotor and install a matched bearing and race set from one manufacture if it's that type of rotor. If it's a sealed bearing type hub and you beat in the outer race by hammering on the inner race or vice-versa it got destoyed via the installation process. It didn't have a chance. Never followed any specific break in procedure other than no hard wheel locking stops for the first few hundred miles. Not to say it isn't worth following a specific procedure based on the type of pads you used. Organic, semi-metallic, Kevlar, etc Lots of different specialty stuff out there now.
One thing I'll add, though it's not quite what you're describing with the little bit of info you provided, A steering/suspension component that's on it's way out can sometimes create a funky come and go type of shake/wobble. When you hit the binders all the force on those components changes directions. A separated belt in a tire isn't always consistent either.