Andreas,
In the /plugins/system/jfbcsystem/jfbcsystem.php file, at line 82, you'll see:
FB.init({appId: '{$appId}', status: true, cookie: true, xfbml: true, channelUrl: '{$channelurl}'});{$subs}
After that line, insert a new line with your code:
FB.Canvas.setAutoResize(100);
In the 4.0 release, we'll have settings for choosing which template you want to use when your page is displayed in a Canvas on Facebook as well as whether automatic resizing should be enabled (inserting the code above).
Hope that helps, and let us know if you run into anything else,
Alex