For some reason this rule is causing havoc in all subsequent rules (none of theme work). What does it mean exactly?
RewriteRule . /index.php [L]
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That rule is apparently supposed to hide the "index.php" part of a visible url. When your working url is this http://www.somesite.com/index.php, this rule will make the browser display http://www.somesite.com/.
There are other ways to do this that may be more effective and less likely to cause problems such as you're experiencing. I did a google search for "mod rewrite RewriteRule . /index.php" to get this info, and most of the pages seem to have some useful suggestions regarding better ways to do this.
I believe it redirects it to root. That way when you go to www.example.com it doesn't show www.example.com/index.php. Helpful for SEO purposes.
Is this a Wordpress setup?
This is a good article over on stackoverflow that explains this.