I finally found the end of skein! It's about 3 days that I'm googling and asking gentoo people trying to solve this annyoing problem I have. In practise, the applications that I minimize into the traybar, once restored, completely loses the postition that I gave to them.
I've so damn noticed that today when I played with Gwibber. It starts placed on the left, I place it on the right, then I minimize it into the traybar, I restore the apps after few seconds and it reappears on the left. With Compiz that didn't happen!
The solution? One frigging line command:
gconftool-2 --set -t boolean /apps/metacity/general/disable_workarounds false
It's quite funny the description of the key "Disable misfeatures that are required by old or broken applications". I think that there must be so many old and broken application nowadays..