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Operating system Linux
Kernel version 2.4.22-1.2199.nptlsmp
Machine Type i686
Apache version 1.3.37 (Unix)
PERL version 5.8.1
PHP version 4.4.4
MySQL version 4.0.27-standard
cPanel Build 10.9.0-CURRENT 82
cPanel Pro 1.0 (RC36)
Long story short, the .htaccess in the /docs directory broke the htaccess/htpasswd, strangest thing. I couldn't find my old .htaccess file, like a moron I deleted it thinking I wouldn't possibly need it it

I have this:
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#Rewrites page.shtml as index.php?page
RewriteCond %{REQUEST_FILENAME} !-f [NC]
RewriteCond %{REQUEST_FILENAME} !-d [NC]
RewriteRule ^(.+)$ index.php?page=$1 [QSA]
I thought it worked, then it didn't.
*** Update
I have now confirmed that it is sitewide, turning on the rewrite passes everything through the cms site because I can enable the custom 404 and that is what is displayed. If I disable the password on the directory then it seems it works just fine, with the password protected directory then ALL paths are passed through it (you can't go to /uploads, you get the same 404). This is NOT the case on a bunch of other sites running cmsms. I am putting in a support request with my host tech. I would be interested in any possible ideas other may have.