I posted an update that should resolve this issue – it was a tough one! There was an issue with the code that detected which rank of each set bonus you had available to you at the start of the optimization.
Note the scores will change a little bit after the update due to the rebalance of the set bonuses on Tuesday.
Thank you! With the gear equipped from the first recommendation, using BiB again says everything is good. I plan to upgrade a shard or two this evening, will see how that goes and will report back if anything seems odd.