Have you check the derailleur hanger? If it's bent, you can get noises in different gear combinations.

Noises can be really hard to locate. You may think it's coming from the rear or cassette but it may not be. I had a weird sound once, took a while to figure out it was from my frame pump that was coming unscrewed and things were rattling. But it was still rhythmic so seemed like it was part of the drive train.

But I get that it is specific to certain gear combinations. So, I too would be focused on the drive train.