... i think so.
it does for me, but mine is a RPM install of FC2, so one never knows.

Same for me too. I'm on Gentoo, LogJam compiled from source.

apparently it is... just click on the tray icon to make the window disappear...

That's exactly what I was trying to figure out how to do. Thanx!

That is one feature I wish it had. Close to the tray, and have a right click menu for the tray to close the actual program. The menu could have other things like "Friends.." and "Friends View" and more that I am not creative enough to think about =P

After school I'll see if I can write a patch and submit it to the devs

I'm not one of the logjam authors, so this should be taken strictly as my opinion. That said:

It's not a bug, it's a feature. Traditionally, "exit" means "I want this program to stop running," with all that implies. Clicking the close box, of course, means that you want to close the window, which conventionally exits the program if that's the last window. (Note that I dislike the behaviour of, say, gaim, or the GIMP, which have a main window upon which all the other windows depend. Close should map to exit only if there are no other program windows. I also like the mac way, where exit is always a discrete operation. (Note that this statement only applies to the Old Days(tm).))

But tray icons are special, not being windows in a ui sense at all. My feeling is that they should be handled by separate programs, with the option to have them automatically close each other on exit.

I've been more exposed to the windows method, but I do agree that there's confusion; and that what you're saying is more precise than what I was saying.

However, LogJam's interface in this respect was a bit ambiguous. I didn't see anything that told me "click on the system tray icon to make the window dissapear".