This is still a problem. Happens occasionally when doing a table Alter. I’ve noticed that when this happens, SQLyog will hang when I try to close it later, rather than closing cleanly.
It’s happening to me randomly too. To close SQLYog, I have to kill the process, (using either xkill or system monitor) and fire off a console command “wineboot” which resets wine, otherwise next time I try and start SQLYog it won’t start correctly.