First of all, congratulations with the new version of your editor. It looks really interesting, even though there seems to be some issues. I guess most of them are cleared when you empty your Joomla caches, as well as the browser's.
Anyway, I am testing the new markdown features of JCE 2.6.0, but I can't seem to get it working. Besides checking the tick mark in the profile's settings, is there something else to do? To you have to work in the editor window or in the code one?