Something has been driving me mad for about 6 months – every time I start Skype on my Ubuntu Linux workstation, the same missed call comes up. I don’t expect that Microsoft will be rushing to fix this any time soon, where’s the money in that?
I found the fix. Stop Skype, load up ~/.Skype/your_skype_login/main.db in SQLiteman and run the SQL query:
update Messages set consumption_status = 0 where type = 30 and consumption_status != 0;
Job done. You might want to back your main.db if you’re paranoid.