Are you currently leveling a new character, using the auto-equip option? I have noticed this as well but I guess I didn't see it as a major fault. I usually just manually do a gear check every 5 levels since auto-equip counts gems as part of the item affix rolls... Doing so takes about 2 minutes on a town run. If you're leveling with that bot at this point of the season I would suggest just using a seasonal powerleveling community.
I put a guide in the guide section about leveling for a new season if you want to take a look.
If you're using this option after already gearing up your desired set and such, you should really disable it since it can break your set bonuses.