After some restarting, and more testing ( to check if the system works, and is more the less reliable ) an unpleasant thing happened today, when linuxmce was "Starting up", i noticed it downloaded updates, and installed them/Applied them automatically.
Guess what got the transparancy issue again, got a little frustrated so i browsed the /usr/pluto/bin directory and found a file called DownloadUpdates.sh, and added another exit;
Did the same thing with ApplyUpdates.sh (just to be sure).
Then i ran the NVIDIA .run file again (from nvidia.com) and did a reboot, hopefully things will be more reliable now.
Didnt use much time researching, but guess it updated my kernel and rendered the nvidia kernel module useless, or it removed some of the nvidia files. either way, the fix wasn't hard.
I want a system which doesnt update itself upon bootup, i'll just do apt-get update myself and write it on my calender for every other week or so