conky & clean desktop

Судя по описанию проблемы, у тебя конки неправильно настроен.

######################
# - Conky settings - #
######################
update_interval 1
total_run_times 0
net_avg_samples 1
cpu_avg_samples 1

imlib_cache_size 0
double_buffer yes
no_buffers yes

#####################
# - Text settings - #
#####################
use_xft yes
xftfont Liberation Sans:size=8
override_utf8_locale yes
text_buffer_size 2048

#############################
# - Window specifications - #
#############################
own_window_class Conky
own_window yes
#own_window_type override
own_window_transparent yes
own_window_hints undecorated,below,sticky,skip_taskbar,skip_pager

alignment top_right
gap_x 100
gap_y 40
minimum_size 182 0
maximum_width 182

default_bar_size 60 8

#########################
# - Graphics settings - #
#########################
draw_shades no

default_color cccccc

color0 white
color1 3465A4
color2 white

У меня такое же поведение в gnome+metacity+gnomepanel. Разве можно настроить, чтобы не сворачивался?

А если

own_window_type desktop

?

Попробуй раскомментировать эту строчку
#own_window_type override

что будет?

З.Ы.
own_window_type:

   if own_window is yes, you may specify type normal, desktop, dock, panel or override (default: normal). Desktop windows are special windows that have no window decorations; are always visible on your desktop; do not appear in your pager or taskbar; and are sticky across all workspaces. Panel windows reserve space along a desktop edge, just like panels and taskbars, preventing maximized windows from overlapping them. The edge is chosen based on the alignment option. Override windows are not under the control of the window manager. Hints are ignored. This type of window can be useful for certain situations.

вроде работает как надо. спасибо!