General help

I'd obfuscate the password salt too (any moderators?).

That's strange, it's not even the permissions of config.php. I'll think about it.

I know they're commented out, but the require for setup.php should be the last thing in this not the debugging switches.

Other than that, I'm desperately hoping you've found some other notices in your logs. I'm struggling really. Just to be completely safe, I would replace your Moodle code with a clean copy from moodle.org just in case something has got screwed up. Also, run a repair of your database tables.

First ... this is a guess - won't hurt to try IF one can edit php.ini.  The fact that apache restart solves the problem leads me to think that maybe the following would fix.

Apologize for the technical in this, but maybe someone more knowledgeable than I can understand/correct if this is in-correct:

Line 69 shows:

$CFG->dataroot = realpath($CFG->dataroot);

Which looks to me like it's setting php's realpath from the config.php file's dataroot variable.

From what I an gather, php's realpath is cached in php which is controlled.  Because of the randomness behavior, wondering if there's an issue with the realpath cache.

Create a flie: realpath.php
with the following contents:


<?php
var_dump(realpath_cache_get());
?>

make sure ownership/permissions belong to the apache user/group, then it the file via browser.

The information will not be formatted, but in browsing one can see expires settings.  On that page that's returned do a find for your moodle directory.  In the example below, the file was placed at the moodle document root in a moodle23 directory.
Find 'moodle23'
One might see something similar to:

 ["/var/www/html/moodle23"]=> array(4) { ["key"]=> int(-1678145344390156167) ["is_dir"]=> bool(true) ["realpath"]=> string(22) "/var/www/html/moodle23"  ["expires"]=> int(1357236007)

Info:
http://php.net/manual/en/function.realpath-cache-size.php
Comment/notes quote:

"realpath_cache_size" is used by PHP to cache the real file system paths of filenames referenced instead of looking them up each time.  Every time you perform any of the various file functions or include/require a file and use a relative path, PHP has to look up where that file really exists. PHP caches those values so it doesn’t have to search the current working directory and include_path for the file you are working on.

Consider editing php.ini
See: http://us2.php.net/manual/en/ini.core.php#ini.realpath-cache-size
Increasing

realpath_cache_size -> 16K which is default

Decreasing:

realpath_cache_ttl <- 120 which is default

In a CentOS Linux server php.ini the following:

; Determines the size of the realpath cache to be used by PHP. This value should
; be increased on systems where PHP opens many files to reflect the quantity of
; the file operations performed.
; http://www.php.net/manual/en/ini.core.php#ini.realpath-cache-size   
; realpath_cache_size = 16k

; Duration of time, in seconds for which to cache realpath information for a gi$
; file or directory. For systems with rarely changing files, consider increasin$
; value.
; http://www.php.net/manual/en/ini.core.php#ini.realpath-cache-ttl
; realpath_cache_ttl = 120

any change to php.ini requires restart of apache service.

NOTE: cannot be used in .htaccess it is PHP_INI_SYSTEM only.

'sprit of sharing', Ken

Which PHP accelerator are you using? I wonder whether it could be a mis-behaving accelerator having issues with the $CFG variable?

It's unusual, but the fact that restarting apache seems to fix it makes me wonder.