New brake tracks need break in period?

[evan326]

So I grabbed some ultegra wheels as a temp set. I had a set of swissstop bxp with my mavic aksiums. When I got the wheels I re-cabled the bike too, so I readjusted the brakes at the same time. After one test ride everything was great. I went through some wet patches of pavement but didn't think anything of it. Next day go on a real ride and the rear is squealing very loudly under braking. Also I'm hearing what I have to assume is wheel flexing under load. I don't see how though as I'm far from a strong rider, and my aksiums never flexed at all.
Could it be just a matter of the tracks needing to wear some? The rear track feels very smooth compared to the front, and especially compared to the aksiums. I've already tried putting a 1mm toe in on the pads, cleaning the tracks and pads with alcohol, and roughing the pads a bit with a file.