I don't believe auto-improve is on by default for mining ships.  Check on that.  (Note: Auto-improve is only available to be selected when they're not sitting on an asteroid field.  If they are, it changed to improve, which will only get them to improve the asteroid field they're sitting on, and only once, after which they'll go inactive again.)

I'm not sure how to help you with your other issue-it may have something to do with the new starbase module management system in TA, but I haven't used that yet.  It's possible you haven't researched the requisite techs for the additional modules, though-but this assumes you're looking at one screen and reading something else, which your post would seem to imply is not the case.