[NiteWave]

P.S. The server is on cPanel and has a remote dedicated mysql server attached to it. Could this be the reason for the slow compilation of PHP scripts?

good point, looks more reasonable -- database warming up has caused the delay.

to verify this, just put a phpinfo() page under the documentroot, if phpinfo() is fast at any time, then the culprit is mysql; otherwise, it may be related to litespeed.