This is what I pulled of the live VSIDO -
sleep 1
{
compton --config ~/.compton.conf &
(sleep 3s && wicd-gtk --tray) &
(sleep 3s && conky -c ~/.conkyrc) &
nitrogen --restore &
## (sleep 3s && lxpanel) &
<snip>
I'd try it like -
<snip>
nitrogen --restore &
compton &
(sleep 3s && conky) &
(sleep 3s && tint2-bottom) &
(sleep 3s && tint2-top) &
< the apps like wicd --tray , no particular order >
Let nitrogen restore the wallpaper before anything else starts and keep it out of the sleep routines - maybe even add a sleep condition to compton. Then start up all those apps after the tint2 system tray is all set to go.
The startup file is read top-bottom and mixing the "sleep" and "&" may be causing some of the problem.
Edit - this doesn't always work - No problem with it on the desktop computer, wallpaper fails to restore on the laptop. Setup similar to what vastone previously posted works.