There is an option that can be used to move where the application save your preferences. If no config.properties file, then that option is not being used. That tells me it is using the standard location, which was suspected since the application complained when the preferences file was read-only.
If the preferences file was being corrupted, you would see two things: (1) the TD would complain on startup that it was unable to load your preferences, and (2) you would see backup preference files being created. When the TD can't load the preferences, it used to simply create a new set of preferences and overwrite the old one (effectively losing your personalized preferences, but the file was corrupted so not much could be done anyway). Now (v3.3) it will copy the original preferences file (prefs.sav) to a file with a timestamp (prefs.sav.20170815-132135) and then create a new preferences file. So you should see some of those files where your preferences file is saved. If not (1) and (2), there doesn't seem to be a problem with the preferences file.
What preference(s) are being reset that makes you think the application is not saving your preferences? Maybe it's a misunderstanding (I know you know the app pretty well but, well, you never know)?