am having a similar issue, I have tried the sugested workarounds to not avail. The error am seeing is very similar and happens when starting the application. no sites have been added and the all the configuration files have been removed from the system.
Thanks for your report.
Can you send me an email, so I can send you back a debug version of WinSCP to track the problem? Please include link back to this topic in your email. Also note in this topic that you have sent the email. Thanks.
You will find my address (if you log in) in my forum profile.