When I hibernate Ubuntu Mate and restart, it does not remember the
Appearance Preferences. I have to reset them and restart Emacs,
Firefox etc to get the font sizes etc that I like.
Is there a way to make Ububtu Mate remember these settings?
Hi @mahmacc 
Strange ...
What is the size of your swap partition and how is your ram setup ?
From what i remember, hibernation will write your memory to swap for sleep.
You have put your finger on a possible problem. My swap should really be bigger. I have 16Gb RAM but only 8Gb swap (on a hard drive partition). However, that is not the whole answer because I see exactly the same problem if I shut down completely and then reboot. The system still knows my appearance preferences because using System -> Preferences -> Appearance immediately shows the right choice.... but it does not enforce them until I have done that, and if (e.g) Firefox has been restarted on reboot I have to stop and start it again to get it to honour the font size etc.
How did you done some apps like firefox to restart if they were opened before ?
It looks like a latency to collect your profile config, so apps and so on are starting not taking them in account. a bit later they are loaded.
You dont have any special thing configured like a software, Security-Enhanced Linux or something that can mess it up ?
Also, Is your desktop layout like the top menu and so on impacted ?
or only the color theme, fonts, ext ?
For themes and so on, where are they stored ? in your home profile /.themes/ or in /usr/share/themes/ ?
Do you use LUKS ?
I believe the Firefox etc start because I long ago used mate-session-save. (I did not log a record of doing that.) When I restart I get the menu etc that I expect. It's only the colour, fonts etc that are impacted. I have files .themes/default/index.theme and .themes/mytheme/index.theme of which the former seems to give the one I wanted, while /usr/share/themes seems to have all the themes not only the one I want. When I invoke Preferences -> Look and Feel -> Appearance I see all the themes etc but if I just hit the close button it has remembered my choice.
I do not use LUKS and I have done my best to turn off selinux (finding it a nuisance)
I have found one link that can help understanding what's up there :
But i believe that the session save is over writing your session to a configuration that is not complete and bad luck this one will be opened at login and not the one you have complete. This explain the fact that getting inside the theme config, only closing something make it work.
Can you try a reboot without session save ?
I never used that before but i see this inside startup apps :
I am no longer using mate's session save but I see the issue having used the startup
option you suggested.
Do this command helps after you have rebooted and the issue is present ?
marco --replace