did you run the copy settings wizard before upgrading. This would have taken all you settings and put it in a file so that you would not have to reset.
best plan of action. is to go ahead and make all the changes to your settings. Then close out the program. Restart it and then verify that everything is as you want.
Then run the copy settings wizard so that you then have a copy of them settings.
If for some reason during the day if you loose a setting you can reset them all back to where they where all saved.
Network connection has some to play around with this. Lots of times if you loose the network connection to a file or folder SolidWorks will go back to the default. I would make sure that your not loosing the network connection also.
Did you ever find the reason for this? I have tried using settings wizard to copy the setting of other users at my company and the same thing happens. I have uninstalled and reinstalled Solidworks 2018 also.
It is getting annoying having to re-load my templates and custom property files every time I go back into solidworks.
have you tried setting them. closing out and then seeing if they stuck?
lots of times I would make a change and then crash and the changes did not stick.
so I started closing out the program and they tend to stay then when I start it back up.