I had gotten a Brooks B17 recently and after much adjusting, things were great except it still I was sore on the right side of my crotch. Eyeballing the saddle, turns out it was not pointed straight. Voila! It's so comfy now. And by getting new PI shorts to replace the old ones, and I never thought riding a bike could be so cushy!
Check the saddle out carefully, and yes, account for "breaking in" your arse again.