This problem occurred with me too. But, only in new installations. In my job, we have 10 computers with Debian Lenny, and when I upgraded synaptic, it worked fine.
But, when I installed the latest release (18- august - 2008) in 2 others computers, I only see the message message box saying that my repos have been modified. No configuration window appears. I used the kernel 2.6.25 - amd64.
