I have the same problem with debian woody package (1.2.5).
I have tried hide / show list but it doesn't change anything.
This started when i finished all download for the first time. The download list was empty. I stopped the mule then restart it and add new download. Since this the list has disappeared. Maybe it's related to this bug.
Sometimes, when i press (continiously) the middle botton or right mouse boton on the transfer windows i can see the list. When i stop presseing it disappeared.
Regards.