Comment 9 for bug 236046

Here's what I found in the changelog

Fixed inability to change trayicon background under Lucid Lynx (Ubuntu 10.04) and possibly other recent distros. Trayicon background is nolonger set, but the icon does now have transparency. Not sure if this is a recent Gtk2::TrayIcon change or whether creating nested eventboxes was the magic solution all along ...

So it'll be always transparent, great!