How do you use the php_include method on individual WordPress pages? I tried adding it to header.php in my theme and that was obviously wrong, it locked down the entire site. I'm wondering where in the theme (or not?) the php_include code needs to be added? Maybe something in functions.php?
What are you trying to accomplish? If you add the code into your template header it would lock the entire site, as you found out. If you want to lock all pages (ie. not posts, but pages) you would edit your theme's page.php. That being said, you're better off using the aMember Wordpress plugin or Ken Gary's amProtect as it will give you a lot more control over protecting your content.