This is a long-standing issue that gets down to how Conkeror's input system works.  There
are various methods of working around it, such as key-kill-mode.  The problem is
aggravated on some sites depending what user-agent string you send them, so you can
experiment with that, too.  This has been an increasing problem because more and more
websites use the keyboard.  Ultimately the input and focus system will have to be
redesigned; some work has been done in this direction in the 'point' branch.