When I drag the red rectangle around in the left container, bits of it sometimes get "stuck" in the right container. I'm doing this in Chrome 11.0.696.71 on Ubuntu 10.04, if that helps.
Just judging by the symptoms without looking at the code, I'd say that perhaps you're only animating the secondary rectangle that mimics the first one when the primary rectangle intersects with the wormhole's edge.
When we move the first rectangle too fast towards the top, some of the events might get missed and the corresponding rectangle doesn't _exactly_ mimic the first one. As no more events are fired, it gets stuck.
You might want to introduce some sort of sanity check for when a rectangle exits the wormhole.
Example: http://www.cl.ly/2B062I2t2k210i0W1m0f
Sonic is over Einstein on the left, but under on the right.