All my bike shorts have some level of padding in them, so I used the same bike shorts on my LHT when I got a Brooks B17. For months I could never get comfortable. I could not seem to sit right on my sit bones, too much pressure up front in the drops. I just kept telling myself I needed to break it in. Then, one day I had to run an errand in a pinch, and just hopped on the B17 with no cycling shorts and was like "Holy s**!" It felt amazingly good. It was probably already broken in at that point because I used the Proofide as instructed and had about 300 miles on it. Since then, I only use compression shorts with NO PADDING on my Brooks. I can do 80+ miles without issue. After that, I understood what all the hype was about. I see now why everyone raved about it. It's tricky to get positioned correctly fore/aft and angled, but when it's dialed it, its like saddle nirvana.
I found the same thing. I had discomfort with my padded shorts. Without them I feel much better. I will add that I found some shorts that actually work well with the Brooks on my last tour though. I have a pair of Bontrager Bellwether shorts that actually feel good. I'm fine without padding though and usually go that route. Padding usually just gets in the way.