If you want the tr to go into the existing tbody then append it there.

If I don't do something extremely wrong here, I think appending to the tbody makes it even worse:

http://jsfiddle.net/q9HYu/3/

This works correctly on current jQuery 2.0 from git, although behaviour of jQuery 2.0b1 is, indeed, erroneous.

Could you advocate to jsFiddle somehow so that they introduce a jQuery 2.x edge option? It would be extremely useful...

Anyway, an updated test case with the current jQuery 2.0.0-pre:

http://jsfiddle.net/q9HYu/7/

Here you can see that the inner structure is set correctly:

http://jsfiddle.net/q9HYu/8/

Btw, working on table instead of tbody works, too: http://jsfiddle.net/q9HYu/9/

Line 315 of manipulation.js handle this:

callback.call(
	table && jQuery.nodeName( this[ i ], "table" ) ?
		findOrAppend( this[ i ], "tbody" ) :
		this[ i ],
	node,
	i
);

(a little OT but related to what I wrote before - I created a ticket for adding jQuery 2.x edge lib to jsFiddle: https://github.com/jsfiddle/jsfiddle-issues/issues/355)