First, are you using Firebug to debug this? In Firebug with Firefox 4 I
can see that at my first attempt to create a table from the navi panel,
there is a js error in the Ajax logic of jQuery. Maybe using a "get"
this way with jQuery is not supported.

I made a suggestion in this thread, about running jQuery in the context
of another frame. For an example, look at the last line of
js/server_privileges.js.

Other points:

- to simplify the code, instead of selecting $('#newtable') and then
looking for the ajax class on the a element, you could put the ajax
class directly on the newtable id and select $('#newtable.ajax')

- watch your indentations (for example in navigation.php)

- you are creating the div id="create_table_dialog" in the "if" and also
in the "else" so its creation should be moved before the "if"

- in navigation.php, try calling js/messages.php after calling
js/functions.js

- when creating js variables, use var; for example, instead of
url = $('#newtable a').attr("href");
var url = $('#newtable a').attr("href");

this way, the variable appears in Firebug and is easier to follow