I guess this is not a pygtk issue, do you have a minimal testcase?

I bet Johan will reassign to GTK+ anyway...

Well, in fact this is not pygtk related, it happens with gtk as well, so please reassign to GTK+

Here is example code to test:

#include <time.h>
#include <gtk/gtk.h>

static GtkStatusIcon *create_tray_icon() {
        GtkStatusIcon *tray_icon;
        tray_icon = gtk_status_icon_new();
        gtk_status_icon_set_from_icon_name(tray_icon,  GTK_STOCK_MEDIA_STOP);
        gtk_status_icon_set_tooltip(tray_icon, "Example Tray Icon");
        gtk_status_icon_set_visible(tray_icon, TRUE);
        return tray_icon;
}

gboolean update_text (gpointer tray_icon) {
	char s[30];
	size_t i;
	struct tm tim;
	time_t now;
	now = time(NULL);
	tim = *(localtime(&now));
	i = strftime(s,30,"%b %d, %Y; %H:%M:%S\n",&tim);
	gtk_status_icon_set_tooltip(tray_icon,s);
	return 1;
}

int main(int argc, char **argv) {
        GtkStatusIcon *tray_icon;
        gtk_init(&argc, &argv);
        tray_icon = create_tray_icon();
	g_timeout_add (1000, update_text, tray_icon);
        gtk_main();
        return 0;
}

Fixed on trunk, will backmerge to 2-14 later.