Alex,
We applied a "maybe" fix for the issue a couple builds ago. Any users with a blank settings.json will unfortunately continue having issues (their settings data is GONE). We distributed custom builds and now public builds with this "maybe" fix and we haven't heard anything bad happening since. However, this was a very intermittent issue that would happen to a very small percentage of systems and we were never able to reproduce, so it's hard to say that we absolutely fixed the problem. It has been a few weeks though since we did this and haven't heard anything new from support, so that "maybe" fix might have actually fixed the problem for good. Customers who had this issue and actually all new version of SM have some more advanced logging to track this issue.
If anyone who thinks they may still be having the issue and you are running a recent build you can check the Errors log for these specific lines.
(This logging won't log for user's with an already blank settings.json. Just new instances of the problem. There might be cases it still logs for users, check my posted update below)
"The UserSettingsFile or the settings property is null--not writing file"
"Password encrypted is null: {EmailAddress}--not writing file"
Obviously user's losing settings is a very serious issue so trust me, we've been trying to hunt it down as much as we can. If you have this problem you can contact our support and they will escalate it as necessary.
Matt Petty
Senior Software Developer
SmarterTools Inc.
www.smartertools.com