Rewrite issue with CI 1.7.2 -> 2.0.2 upgrade

[eluser]kettch[/eluser]
I've done a diff of all the files in /system compared to the default 1.7.2 files and they are all identical except for the obvious /system/application files so I'm not missing any CI customizations when I moved to 2.0.2.

Here is my RewriteLog output: http://pastebin.com/b8T8Hu1D

You can see the rewrite gets applied correctly and ends up with:

http://<address>/<subdir>/index.php/page/id/faq

However, this returns a 404 whereas manually typing in the exact same URL into the browser returns the content correctly. The RewriteLog when using the manually typed-in URL has all of the same output except it obviously skips the need to go from <view> to /page/id/<view>.

Does anyone have ideas? I'm getting no errors in the Apache logs or the PHP logs at all other than the generic 404 in the browser. Again, this issue only occurs when I upgraded from 1.7.2 to 2.0.2. If I revert all of the 2.0.2 CI files to 1.7.2 then it works correctly.