Rubber boots--totally possible. Sounds like the mechanics know their stuff, so, I think it's all good. The chatter is an independent issue and it's a good bet it's pad deposits.
There's this guy on the forum here who has a great piece on braking techniques. Have
a look. I found applying what I learned very helpful in both being consistent and getting the most out of managing my brakes. (Btw, that guy is "The Hack"
.)