The only errors we ever got were either "SERVICE UNAVAILABLE" on a webpage or the PHP log file (we called it php_error.log) would have an entry something along the lines of:
PHP Warning: PHP Startup: Unable to load dynamic library
'G:\PHP\ext\php_mysql.dll' - Access is denied. in Unknown on line 0
PHP
Warning: PHP Startup: Unable to load dynamic library
'G:\PHP\ext\php_mysqli.dll' - Access is denied. in Unknown on line 0
We figured it was permissions related since it worked OK once the Administrator user was responsible for the application pool. Switching back to NETWORK SERVICE or IWAM_<machinename> resulted in the PHP errors in the logs again.
Obviously IIS5 has no application pools so in reverting to the isolation mode we ruled that bit out and it all worked OK. Annoyingly though we've been told today that we're to switch back to WAMP on an XP Pro box and all the work we've done over the past two days (which obviously resulted in a working system in the end) was for nought. Poo
Oh, and for reference we were using PHP via ISAPI and not CGI, the correct PHP.ini file was being read and all changes were reflected in phpinfo(). The ONLY thing that wasn't working properly were the MySQL extensions. EVERYTHING else worked OK, including other extensions