Having run into a similar issue, I believe I've come up with a workaround.

Since Flash seems to steal control of the cursor, use flash to set the cursor.

1. Create 2 functions in your flash movie. setHand() and unsetHand(). setHand() creates a clear layer over the whole flash movie with useHandCursor=true. unsetHand() removes the layer.

2. Call setHand()/unsetHand() for all the elements that need the hand cursor using javascript. If you're using jQuery it might look something like this:
$('a').hover(
function(){ flashMovie().setHand(); },
function(){ flashMovie().unsetHand(); }
);

And viola! The pointer cursor is back.