I've got the latest git master versions of empathy, gtk+, and gnome-shell installed, and I hit the following warning a few times each time I launch Empathy. Empathy's tray icon also appears as just the upper-left quarter of the icon (ie, a quarter-circle).

Here's the backtrace:

Gtk-WARNING **: gtk_widget_size_allocate(): attempt to underallocate toplevel GtkTrayIcon 0xa3c020. Allocation is 24x24, but minimum required size is 48x48.

Program received signal SIGTRAP, Trace/breakpoint trap.
g_logv (log_domain=0x7ffff016571b "Gtk", log_level=<value optimized out>,
    format=0x7ffff0230598 "gtk_widget_size_allocate(): attempt to underallocate %s%s %s %p. Allocation is %dx%d, but minimum required size is %dx%d.",
    args1=0x7fffffffd958) at gmessages.c:559
559               g_private_set (g_log_depth, GUINT_TO_POINTER (depth));
(gdb) bt

+ Trace 227602