Having set up 2 step verification for additional security, a number of apps initially "break".
Calibre was one of them, as I have it set up to send articles to my free@kindle account via Gmail.
This post suggests it's not possible to change this - http://oldbugs.calibre-ebook.com/ticket/9415#comment:1 - but in fact it is, by setting up an application specific password and entering THAT in Calibre, not the standard Gmail password