I haven't run into this issue in a long time.
Usually the causes are when you log in again after shortly logging out of DDO and the client process of the previous DDO client was still shutting down. So I've often staggered my log in when going with multiple clients by seeing the game client pop up first before attempting the next one.
Incidentally, this is also the same process that I utilise to have a reduced chance of sound not loading in properly for a particular client. It can still happen, just much less likely. Although in this case it is through waiting until it's about to load the character selection screen before I hit enter to log in. Also, unsure if stated here or in previous linked posts, but leaving the login client part way loaded (not yet selcted server) whilst you do other things, tends to cause it to end up with sound issues.
Patience in short, is the way to least likely experience these issues.
Finally, I am unsure if this still works, as again it's been a long time since I ran into this issue (was still on Windows 7 and 8/8.1 when I needed to do this). I "think" the preferences file hasn't been reset to defaults yet and you can navigate to the folder and make a copy of it. Then clink on yes/no, whatever and let it reset or change settings. Then close the login client. Wait a second or two, then delete the newly default preferences file, and replace with your just made preferences file with the old settings and keybindings to continue with how it was before. I believe the other option that was often used to mitigate this issue was to have a backup of the preferences file on hand once you have everything the way you want to and then replace as needed whenever it happens again.
Note, I'm not saying it shouldn't be sorted out by SSG better, just that until they do, we players need to have our own ways to tackle issues. Hope these helps anyone in the mean time.
J1NG