I want to report another common reason matlab on linux would be unable to read the preferences file. I often run matlab over a VPN I establish to the head node of a computer cluster. I then use matlab to submit parallel jobs to the compute nodes. Sometimes, I'll have more than one VPN tunnel established at once- one from a work computer, then later another from my laptop, or maybe from a different work computer. None of my tunnels can see the other's applications, so I end up running multiple copies of matlab operating out of my same user folder.
If one matlab opens the preference file for writing, perhaps because I made a change to the window arrangement, then when I attempt to open the second matlab through a different terminal, I receive this error.
If this applies to anyone else, the solution is that if you change the preferences in one instance of matlab, reboot this one before trying to open other instances. If you already have multiple instances running when you change the preferences from one instance, the others will stay open, but will throw this error when you try to reboot them.