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I know this question is kind of a WP and kind of a webmaster issue. I am really stuck troubleshooting how IIS is handling rewrites and permalinks. Anyone that can offer an explanation or demarcation of the topic would be helping out a ton.

Background:

Tons of WP (and non WP) sites on a subdomain (at big company). I must use subdomain and cannot be issued any other URLs. So all of my sites sit in sub directories. I know this is not optimal but have no choice.

All of my WP sites sat at least one directory level up from root - they were all working fine given that I used a permalink structure that included index.php/%whatever. Everyone is happy.

The root of the subdomain was a redirect to another site. They asked me to close the redirect and take our sandbox/mainsite and move it to root. I made backups of files and database tables and hastily moved site to root...

Big problems...

Basically any site that I installed WP on more than a few weeks ago refuses to work with any sort of permalink structure. Default works. Anything else is jacked up - sometimes they work in Chrome/FF but not IE (it is not a cache issue), sometimes if I change the permalink on WP backend I cannot reach anything but homepage, sometimes I see the permalink url when hovering but it takes me somewhere else, sometimes media paths were messed up (so site looks like it is missing css).

Basically I have screwed up the entire rewrite process on the server - without making one change to IIS. What makes this more frustrating is that I do have a few WP sites that I just installed that the permalink stuff works perfectly on... Also all non-WP sites are working fine of course.

I can give you all the info you need but site is intranet - but could do screenshots if needed.

Where do I start troubleshooting this?

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