I mentioned this on twitter last night (from @frngtstc) but didn't have time to follow up. I got some surprising results this week when I ran my gear through BiB. I'm not saying they are wrong, because I don't know and haven't simmed these combinations myself, but my gear hasn't changed a lot (got 940 legs from weekly chest) yet the results are pretty different, I thought I'd at least share them.
Here is the string for my guardian set. Note that I have Luffa's locked in. I found that if I changed the strategy from "Raid Boss (Mythic) - conservative blend" to balanced that it dropped the T20 bonuses, which shocked me. I'm just filling in as a tank right now so I don't know the spec well but it was the first time it suggested dropping the defensive tier bonuses.
Then for feral, I had my single target gear equipped and changed the strategy to multi-target, which is the set I use for Harjatan and Sassz'ine. It recommends dropping 4 ilevels, breaking the T20 bonuses and getting the T19 2p bonus back. Again, I'm not saying this is wrong but it is very different from what was recommended last week.
Does it seem BiB is working properly? I'll give the gear a shot.