In fact, reinstalling caja and even the entire mate desktop worked for me. I first tried the options mentioned before, except for the github thing wich i think is very dificult for me, an inexpert user.
My original installation was Mint 16 Mate, but recently installed other Desktops like KDE and Xfce, so maybe the problem originated from the installation of them. I set up Xfce as my default DE with autologin and everything was ok until yesterday when i tried to login with Mate and a lot of X-caja-desktop windows popped up.
I've read other posts but nothing worked, and to tell the true i don't understand that thing from github so i decided to try the "reinstall" approach and IT WORKED, HA !!
What i did was to login with Xfce and there i opened the software manager and uninstalled caja and caja-commons, then i logged out and tried to login with MATE, but it suddenly dissapeared from the menu of desktops in the MDM login screen. So i returned to xfce and again in the software manager i uninstalled the entire mate-desktop. I rebooted the system just to feel sure that everything worked right (sorry i come from windows) and then i (re)installed mate-desktop again in the software manager and also caja and caja-commons.
Then i re-logged with Mate and Voila !! my entire desktop as i left was there !! NICE
I didn't lose any icons or files i left in the desktop, everything was there, my entire configuration was intact, except for two duplicated icons: my home folder icon and system icon.
I think this is a different aproach from the other ones in this post, but i hope the users who encounter this problem could fix it with this "reinstall" solution, without having to enter lines of code or knowing where is this or that thing. Greetings.