I'll look at this some more, but did you just say it works fine if you specificy the php ini file in Apache's config using the PHPIniDir directive? Then why not let that be your solution?! I understand wanting to know why, but there is a LOT of stuff about a lot of services/configurations that I never fully understand--I just know I figured out enough to get it working and moved on. Placing a PHPIniDir directive in the Apache conf is not a "messy hack" or anything, so I would not feel bad using it...problem solved.