[wp-hackers] Help needed with two issues on established WP install

[Vogel, Andrew (vogelap)]

Hey gang.

Yosemite, petit, moshu, and vkaryl have all offered assistance to me on
these problems, but we've reached a stand-still and the problems
persist. So I am turning to the Hackers group in hopes of getting these
two persistent problems resolved once and for all.

I've been running WordPress at www.drewvogel.com since June 2005 on an
FC5 box (kernel 2.6.17-1.2174_FC5) that I host. Since installing
WordPress 2.0.4 I've been having trouble in the following areas:

1. I've got WP-Cache (2.0.17) installed on my server, but I had to
disable it because it would work if the page was hit once (when the
cache page is generated), but failed to display (only a white screen is
displayed) if the page is hit again. I have tried the "ob_end_flush();"
instead of "ob_end_clear();" fix with the same disappointing result.

2. I've got my Permalinks set to Custom ("Almost Pretty") and
"/index.php/%year%/%monthnum%/%day%/%postname%/". The goal is to get rid
of the "/index.php" from my permalinks to make them "Pretty". As long as
I do not visit Options->Permalinks, my site functions as expected.
However, if I VISIT Options->Permalinks, my site's permalinks stop
functioning unless I set them to Default (I don't even have to click
"Update Permalinks Settings"; simply visiting the Options->Permalinks
page breaks permalinks), which breaks internal links in my site. This is
100% reproducible. The .htaccess file is 664 and writable by the server.

I have also noticed that rolling back -- that is, restoring the backup
of my .htaccess file, adding "/index.php" back to the permalink, and
restarting the server -- did not return the site to working order.
Simply VISITING Options->Permalinks is enough to cause the site to stop
working, no matter if I "Update Permalink Structure" or not. I end up
having to empty and restore my WordPress database from backup! 

I've replaced the classes.php and functions_post.php files with the
latest copies in this thread
(http://wordpress.org/support/topic/54340/page/2?replies=52) and done
all the steps here:
http://codex.wordpress.org/Permalinks#Fixing_Permalink_Problems. I've
followed all the steps on
http://codex.wordpress.org/Permalinks#Fixing_Permalink_Problems, but my
.htaccess is still never updated. I've followed the steps here,
http://wordpress.org/support/topic/58389. This issue is scary because
simply visiting Options->Permalinks hoses the site.

The .htaccess looks like this:
# BEGIN Url Rewrite section
# (Automatically generated.  Do not edit this section)
<IfModule mod_rewrite.c>
    RewriteEngine On

    RewriteBase /

    RewriteCond %{REQUEST_FILENAME} -f [OR]
    RewriteCond %{REQUEST_FILENAME} -d [OR]
    RewriteCond %{REQUEST_FILENAME} gallery\_remote2\.php
    RewriteCond %{REQUEST_FILENAME} !/wp-gallery2\.php$
    RewriteRule .   -   [L]


    RewriteCond %{THE_REQUEST} \ /d/([0-9]+)-([0-9]+)/([^\/\?]+)(\?.|\
.)
    RewriteCond %{REQUEST_FILENAME} !/wp-gallery2\.php$
    RewriteRule .
/gallery2/main.php?g2_view=core.DownloadItem&g2_itemId=%1&g2_serialNumbe
r=%2&g2_fileName=%3   [QSA,L]

    RewriteCond %{THE_REQUEST} \ /f/([^?]+)(\?.|\ .)
    RewriteCond %{REQUEST_FILENAME} !/wp-gallery2\.php$
    RewriteRule .
/wp-gallery2.php?g2_controller=permalinks.Redirect&g2_filename=%1
[QSA,L]

    RewriteCond %{THE_REQUEST} \ /v/([^?]+)(\?.|\ .)
    RewriteCond %{REQUEST_FILENAME} !/wp-gallery2\.php$
    RewriteRule .   /wp-gallery2.php?g2_view=core.ShowItem&g2_path=%1
[QSA,L]

</IfModule>

# END Url Rewrite section

# BEGIN worst-offenders
Deny from 193.93.237.16
...
Deny from 193.93.237.30
# END worst-offenders

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>

# END WordPress

These are extremely frustrating issues! Can anyone help with any of
them? Thanks in advance!

The history of these two issues can be found in these two threads:
http://wordpress.org/support/topic/83832 and
http://wordpress.org/support/topic/58389. 

Thank you in advance for your assistance!

-andrew vogel
Manager of Professional Programs
University of Cincinnati
College of Pharmacy