I have tried seemingly everything but nothing seems to survive a reboot.
I have made a .Xmodmap in my homedir that remaps the windows key as F14 so I can use it to launch synapse.
I am able to apply it when already logged in using the command:
xmodmap /home/shimi/.Xmodmap
but any method I have found online to make it permanent doesn't work.
The first time I log in after making that file I'm asked by MATE if I want to load it and if to ask every time. I load it and tell it not to ask again. It doesn't work the next time.
I tried making a bash script that runs said command, make it executable and add it to startup applications, but that didn't help either.
tried adding the line to .xinitrc, to /etc/X11/Xsession, to /etc/mdm/Xsession.. absolutely nothing seems to work.
However after I'm logged in and everything loads, opening a terminal and running the command successfully remaps the key.
I'm completely baffled.
Any idea how to make this change permanent?

