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0e1f616
(Get the code!)
My desktop is continously upgraded since feisty, too, while my laptop was freshly installed with gutsy tribe 2.
So when I come home tonight, I'll take a look at possible differences in the configuration files.
Another thing (this is really farfetched, but I'll mention it anyways):
I had a (some time ago) a similar effect using VDR (the Digital TV application).
Started from gnome-terminal, it would occasionally freeze gnome-terminal, and when trying to print the next debug message to stdout/stderr, it would freeze because g-t would not print them. AFAIK, update-manager and synaptic use the same codebase for displaying the terminal as gnome-terminal does. So, I'll try to find out what happens when I upgrade from xterm rather than from gnome-terminal
This might be unrelated, but I have a strange gut feeling about this...
Ciao
Martin