I had the same issue, export settings, pause after rounds and payout settings were missing ... using beta 4.
It's hard to understand how some preferences could change (or be reset) and not others. You mention "payout settings". What do you mean by this?
We had storm damage to our house in April so we haven't played since then, until last Saturday so its possible that all the settings were reset. I may have fixed some of them because I know I fixed some layout things. During our tournament the pause after rounds were off and after the tournament all the export settings were reset. I mentioned payout when I should have said prize, I setup the prizes years ago and basically haven't touched them since, I thought I configured the default template but its possible I had a custom template which I couldn't find.
Other than those minor things the tournament with beta 4 ran great. I was one of the people that experienced all the problems with the last version so this was a welcome change. You did a great job and your hard work to get everything fixed is greatly appreciated.