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There is a bug with the up and down buttons in iMenu which manifests itself if register_globals is turned off in PHP (and that's been the default setting for a while now).
The up and down buttons don't work because the move() function in the admin/index.php file relies on $id and $weight being defined from params sent through the GET method, but that file does not explicitly define params sent from GET. Therefore, if register_globals is off, then the up and down buttons don't work.
To fix, just add these two lines (or similar) right before the call to im_admin_move (around line 32):
$id = $_GET['id'];
$weight = $_GET['weight'];
--Julian