I get intermittant loss of connection (not for any period of time - just an individual query) on my MySQL database accessed from a web server. Is this the connection or something that MySQL does every now and again?
This does happen occasionally if you overload it with data from the client. It often happens when you paste a huge query into a console window for example. If this is the cause, you maight try and increase the 'max packet size' option in the MySQL config.
There are also problems with some MySQL setups that customised caching. Whenever a DDL statement is executed the connection is briefly 'reset' while the database structure is recached.