How do I.. When changing passwords I get a popup to generate the password

Having trouble fully understanding your post, but from the wording of your topic title and some of your described symptoms, I gather that you are using the inline pop-up menus to autofill passwords, and that newly generated passwords (created using the pop-up suggestion) are not being saved in your vault. If that is a fair description of the problem you are facing, then the following bug fix (which was merged last week, and should therefore presumably be available in the next release) may offer some relief:

 

In addition, you may want to avail yourself of the configuration modification that is suggested in this comment: