When connection lost to server, reconnect often takes a long time to reconnect, over 77,000 ms according to info in History tab! We have seen the same thing with MySQL Query Browser so it is not a problem with SQLyog, but I am hoping somebody can give me a tip on how to solve this since it is very disruptive.
We are using a Windows 2008 64-bit server and MySQL 5.1.4x and the Windows firewall. The Session Idle Timeout is set to 128,800 seconds so that it is not the reason for the disconnect.