I'm having this problem too now that I'm using Gnome again.

However, I think it might be related to somethintg I noticed in KDE:
When I restart plasma-desktop, all system tray icons reappear in the system 
tray, except xchat which appears in it's own mini window (only an xchat icon + 
titlebar).

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xchat tray icon doesn't appear if xchat is in Startup Applications
https://bugs.launchpad.net/bugs/445509
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