The bug occurs again since a few days, so I reopen the report.

I have more information about this bug. See above the updated bug description, and below the debugging output when the bug occurs:

$ alltray -d
click_mode
win->notray: 0

(alltray:29600): Gdk-WARNING **: Can't confine to grabbed window, not native
found alltrayable windowhide
get_window_icon with size request: 30x30
read_rgb_icon  --> ok
command_menu->len: 0
have manager window.... now creat_tray.....
get_window_icon with size request: 24x24
read_rgb_icon  --> ok
update window title
net_wm_visible_name failed
title: Liferea
win->title: Liferea
theme is: Clearlooks
theme name: Clearlooks
theme_file: </home/nom/.themes/Clearlooks/metacity-1/metacity-theme-1.xml>
Failed to read theme from file /home/nom/.themes/Clearlooks/metacity-1/metacity-theme-1.xml: L'ouverture du fichier « /home/nom/.themes/Clearlooks/metacity-1/metacity-theme-1.xml » a échoué : Aucun fichier ou dossier de ce type
theme_file: </usr/share/gnome/themes/Clearlooks/metacity-1/metacity-theme-1.xml>
Failed to read theme from file /usr/share/gnome/themes/Clearlooks/metacity-1/metacity-theme-1.xml: L'ouverture du fichier « /usr/share/gnome/themes/Clearlooks/metacity-1/metacity-theme-1.xml » a échoué : Aucun fichier ou dossier de ce type
theme_file: </usr/local/share/themes/Clearlooks/metacity-1/metacity-theme-1.xml>
Failed to read theme from file /usr/local/share/themes/Clearlooks/metacity-1/metacity-theme-1.xml: L'ouverture du fichier « /usr/local/share/themes/Clearlooks/metacity-1/metacity-theme-1.xml » a échoué : Aucun fichier ou dossier de ce type
theme_file: </usr/share/themes/Clearlooks/metacity-1/metacity-theme-1.xml>
normal found !
right_titlebar_edge: 4 !
icon_window_configure_event: 24x54
update_tray_icon: real plug size: 24x54
get_window_icon with size request: 24x24
read_rgb_icon  --> ok
property notify
icon_window_configure_event: 24x54
update_tray_icon: real plug size: 24x54
get_window_icon with size request: 24x24
read_rgb_icon  --> ok
gnome unmap notify
property notify
property notify
icon window press event
show
first click
gnome map notify
one under root function
current runner: 69206019
current runner: 37124428
target_our_w: 1274, target_our_h: 916
  Relative upper-left Y:  25
map notify
mapped
check if.......
inside
visibility notify state: 0
property notify
property notify
motion notify: 1244 19
outside
motion notify: 1242 18
outside
motion notify: 1240 17
outside
motion notify: 1240 16
outside
motion notify: 1239 20
outside
motion notify: 1243 913
icon window press event
hide
property notify
gnome unmap notify
property notify
property notify
icon window press event
show
check if.......
inside
gnome map notify
visibility notify state: 0
property notify
property notify
property notify
motion notify: 1243 20
outside
motion notify: 1241 20
outside
motion notify: 1239 19
outside
motion notify: 1235 17
outside
motion notify: 1230 16
outside
motion notify: 1223 14
outside
motion notify: 1213 11
outside
motion notify: 1199 8
outside
motion notify: 1185 5
outside
motion notify: 1169 3
outside
motion notify: 1151 0
outside
motion notify: 764 16
outside
visibility notify state: 1
motion notify: 426 913
motion notify: 1121 912
icon window press event
active window id 77594628
show
check if.......
inside
visibility notify state: 0
property notify
motion notify: 1244 23
outside
motion notify: 1272 584
motion notify: 1270 607
motion notify: 1255 914
icon window press event
hide
property notify
gnome unmap notify
property notify
property notify
icon window press event
exit_call
destroy_all_and_exit
close window
$