I have my prot gear equipped. When I import my gear, the retribution setup shows I have my prot gear equipped. All good so far.
However, if I change to my prot setup, it says my ret gear is equipped.
Could you post a snapshot of your setup so that I can see all of your settings, etc.? Instructions on how to do that are in this post:
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When you import your character, we auto-detect your active spec based on your chosen talents. We will only update the equipped gear for a Best in Bags setup if it has that spec, or has the exact same talents as you currently have in-game.
So if you want the website to update the currently-equipped gear for your protection setups, you would need to switch to those talents in-game, then export to the website.
You missed that BOTH specs are showing the wrong gear. One of them is always selected.
Could you post the string of data that you copy from the in-game addon to the website? With that I can replicate doing your import and see if it is working as intended.