Have you tensioned your Brooks? After you ride the Brooks for a lot of miles, it will start to sag a bit more than you'd like, and you need to tension it. I had to tension mine after about 40,000 km. Use your little Brooks spanner and give the nut a half turn or so to tighten things up.
And if you really figure you've been riding on your soft tissue with a Brooks, I'd guess that the Brooks you have isn't wide enough for you. The Brooks saddle should have you riding on your sitbones ... much more so than any softer saddle.