What else causes "Commands out of sync"?

[Steven Small]

My application uses a remote connction to both a file server and MySQL. There is an encrypted socket for each link. The application doesn't try to use the database link during file transfers, as there may not be enough bandwidth, particularly over a VPN connection. After the file transfer, the next attempt to access MySQL sometimes produces the "Commands out of sync; you can't run this command now" error. If I wait long enough, the problem goes away and I can access MySQL again.

Here's the link to the documentation about this error http://dev.mysql.com/doc/refman/5.0/en/commands-out-of-sync.html. The documentation gives an example of what could cause the error, but I am not using any of the functions listed in the example.

Does anyone have a complete list of what can cause the error?