we had the same problem and with fcgid the script from the web based wizard was running again after it timed out creating the table already exists errors. Using cpanel to manage apache we have /usr/local/apache/conf/php.conf that adds configuration for fastccgi php. Adding these settings and restarting apache worked:
IdleTimeout 3600
ProcessLifeTime 7200
MaxProcessCount 64
DefaultMaxClassProcessCount 8
IPCConnectTimeout 300
IPCCommTimeout 7200
BusyTimeout 300
What will be a problem is down the road if we use easyapache3 from within cpanel it is going to override this php.conf :-(
--Vince
