[CentOS] Web pages time out after server rebuild

Wed Jan 21 15:14:43 UTC 2009
Rob Kampen <rkampen at kampensonline.com>

Hi All,
I have an old (2004) Intel based server with 4G of ram running
Linux ndgonline.net 2.6.18-92.1.22.el5 #1 SMP Tue Dec 16 12:03:43 EST 
2008 i686 i686 i386 GNU/Linux
fully up to date using centOS rpms for apache, php, and mysql.
I have just changed from dmraid to md raid for the OS on mirrored 80Gb 
SATA drives. (long story for another time)
Mysql lives on a Intel hardware raid 5 controlled array - as is has for 
four years.
My application has not changed and also runs just fine on another server 
(although this one is 64 bit) that has a mirrored mysql database 
replication from this one.
I have compared apache conf files, my.cnf and all appears well.
The page that times out on our firefox browsers after 30 seconds does 
have a series of complex mysql queries.
There are no log messages other than ssl_error_log that shows:
PHP Fatal error:  Maximum execution time of 30 seconds exceeded in 
/var/www/htdocs/ndg/includes/customHandler.inc on line 87
the line number varies as does the file name it reports.
It will serve pages that only have a few records, yet on my functioning 
server even the large pages return over the internet in less than 2 seconds.
So I'm thinking not enough memory? - but it was working well last Monday.
something slowing mysql?? - all other queries in this app appear just fine
php having issues?
How do I get some extra log info to track this down?

Kind regards
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