Disc Brake Question on Venge Vias - Help!

I have a 2018 S-Works Venge Vias with SRAM Red Etap groupset. I bought the frame separately from the groupset and had it built up at my bike shop, along with Roval CLX64 wheels.

The brakes are giving me issues. The SRAM Red rotors/pads were both brand new when I had the bike built, but gave some rubbing noise to begin with and the brakes were a bit noisy. This seemed to get worse over the initial 100 miles of riding, especially in the front brake. If I pulled the front brake it would let out a loud noise… I let off slightly and reapplied the brakes to make them nice and quiet.

My shop took off the rotors and pads, cleaned them, “torched” them to get rid of contaminates and gave the bike back. I did a 90 mile ride and the noises were back pretty quickly. The shop suggested I changed out the SRAM Red rotors/pads for Dura Ace Rotors.

Yesterday I got the bike back with new (Dura Ace now) rotors and new pads. I did a full “bedding” process last night with a gradual hill (get up to speed, slowly pull brakes until nearly stopped but don’t actually stop, then go around the block and do it again. Repeat 8x).

Still the brakes “Pulsate” a when I pull them gradually. Is this something that will get better over time, or should I take it back to a shop? If it’s not going to get better, what’s the actual issue?
Could the disc brake not be mounted correctly? Wheels/hub is bent or something?

Thanks for any help. This is frustrating as it’s a very high-end bike and high-end components and I only have about 240 miles on everything.

Sounds like the pads aren’t making square contact with the rotors or they aren’t centered and one pad is hitting first then flexing the rotor into the other pad.

I don’t have disc brakes but personally I would take it back to the shop where you had the work done and ask them to assist. If your LBS is not up to the task I would try and find one that works on top end bikes.