We don’t change the talents used for optimization when you import. Because we allow you to have multiple setups per spec, it would be awkward if we kept changing them on you – there wouldn’t be a good way to know which of your multiple setups to change. Also, people often have their talents slightly different in-game when e.g. doing solo stuff compared to what they use for raiding and optimization, so it would be irritating if we overwrote those.
You should manually choose the talents that you want to use for optimizing with each of your setups. We copy your current talents for convenience the first time you load a character.
As for the gear recommendations, I think you just need to get a few more gear options, or maybe need to reset your gear information in the addon. Instructions on how to do that here: