Hi Kovid,
The first one seems to be a bug -- I'll check with our devs. (EDIT: did you see our docs?
http://www.mathjax.org/docs/2.0/typeset.html -- MathJax.Hub.Queue(["Typeset",MathJax.Hub]); is the official way, unless there are serious reasons not to).
Thanks for the second one. Scrolling is usually tricky since MathJax changes a lot on the page, so I'm not sure if this is just our known problem or something more. Could you file a bug report on github.com/mathjax/mathjax about it?
IIRC, calibre viewer uses webkit, so this is likely a generic issue that we would like to fix.