Those multiple copies are indicators that Thunderbird has been periodically interrupted when doing updates, causing a new copy to be created. I think you can (with TB not running) rename the one with highest number to prefs.js and remove the other ones. Restart thunderbird and then exit to verify that it didn't create a prefs-1.js.

I was finally able to solve the problem ! This is probably the explanation for several reports of changings to being saved. What happened was somehow my prefs.js file was set to read only. It would not display in windows explorer so it appeared to be missing. The way I corrected this was the following:

1 Locate the Thunderbird Profile Location from Thunderbird Help 2 Exit Thunderbird 3 Enter CMD from Windows Search Bar 4 Change directory to Thunderbird Profile 5 Use the Attrib command: Attrib -s -h -r prefs.js 6 Leave the CMD window open 7 Restart Thunderbird and make the changes you want 8 Exit Thunderbird 9 Go back to your CMD window Dir command: Dir prefs.js 10 You should see a new write date and time on your prefs.js file which means your changes have been saved