php.ini won't help you there, it's your mysql configuration that are wrongly configured or you simply have reach the limit of your setup. I'll guess mysql is set up wrong since ez publish tends to wear out php/apache before mysql, if mysql is set up correctly.
Mysql comes with quite conservative settings by deafult, so there is a lot you can do. How you set it up depends highly on the server, first and foremost how much RAM it has. Since you really don't want mysql to swap it's memory cache to the hardrive..
Here is the more or less the settings used on a linux box that had the same problem recently since the hoster used default mysql settings:
