Since Classic doesn’t have the concept of a “spec” built in, it’s a little more difficult to update when importing a character. We recently made a change that should help out with this, but first some general info:
Normally, the way Best in Bags works is that you create multiple “setups” on the website. You can see a list of them on the left, and put them in priority order so that e.g. a lower-priority setup doesn’t change enchants on items that you have set for your higher-priority setups.
For each setup, you specify the talents that you wish to use in Step 1 (simply click on the talent summary to bring up the full tree and change them). These talents can be different than what you have chosen in-game. The important thing is that you choose the talents that you will ultimately use when raiding (or doing whatever content you are optimizing for).
The first time you use the site, we automatically populate the talents from what we saw on your character. After that, you have to change the talents manually whenever you wish to use something different. We won’t change or overwrite them when you import. We do it like this because it would be pretty irritating if we kept overwriting your talent choices all the time. For example, what if you had two setups for your Enhancement Shaman with two different talent builds… the whole point is that we don’t overwrite those talents when you import, since you want to maintain two builds with different talents.
As for updating your equipped gear when importing, we use a couple rules to figure out which of your setups to update. Firstly, if any of your setups on the website have the exact same talents chosen as those that you currently have chosen in-game, we update the equipped gear for those setups. Secondly, if you have a majority of points in one tree, e.g. Enhancement, we update the equipped gear for any Enhancement setup that you have created.
Hopefully that information helps explain how the import process works for Classic.
Short version: if you can’t get the gear on a setup to update on import, change the talents on the setup on the website to match your current talents in-game, then import. You can always change them back after importing.