Hi immersionfx,

> Will it be able with newer versions of JackStart to run from within the
> webpage (like Flash) instead of opening an own window?

Yep, the new version will support to run your game within the page.
There's screencast demo here: http://centillex.com/jack/jackplet.swf

A bit more to say, the non-embedded version allows you to enable the full-screen mode, while the embedded version runs your game inside the browser (so that you can, e.g, put some ads around).
The different versions serve different purposes.

Cheers,

Chanwit