PHP functions which map to access() libc function are looking in wrong directory under Apache2. Simple example:
$FILE = "test.php";
file_exists($FILE);
is_readable($FILE);
fopen($FILE, "r");

produces such output from strace:
access("test.php", F_OK)                = -1 ENOENT (No such file or directory)
access("test.php", R_OK)                = -1 ENOENT (No such file or directory)
open("/home/httpd/html.michal.waw.pl", O_RDONLY|O_NONBLOCK|O_LARGEFILE|O_DIRECTORY) = 22

Also note that:
[root@woland html.michal.waw.pl]# l /proc/16627/cwd
lrwxrwxrwx    1 root     root            0 11-11 13:57 /proc/16627/cwd -> /
[root@woland html.michal.waw.pl]#
where 16627 is a PID of httpd process which was traced earlier.