Flops,
Not my cuppa, but – as a public service

– I downloaded (after a quick research) Bombono. Now, my puter is rather slow, so the actual encoding is a s-l-o-o-o-w process, BUT:
I created a project with three vids... one .wmv, one .avi and one .flv. It had no objections with my choice of formats. Started the encoding process con mucho gusto.
There is the menu(s) creator, and options for burning/iso creation etc.
Might be worth a try... dunno. Not my cuppa, as I said.
NB: I installed the development version – a slightly older version available in "normal" repos:
https://launchpad.net/~muravjov-il/+archive/ppa
Home page:
http://www.bombono.org/cgi-bin/wiki/