I have been experiencing this same phenomenon. I am running the current version of gnome-terminal in lenny as of this morning (July 17). It seems to mostly happen then gnome-terminal has been running for a while (over a day or so) and it doesn't seem to matter what you change in the profile, almost all options seem to have the same behavior. Occasionally not all terminals will close, but usually all do. Also, it seems to happen less often when fewer terminals are open.
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