g1smd - 7:38 pm on Mar 21, 2011 (gmt 0)
You said: "the redirects should not be touching..."?
I actually said: "The Regeneration code should not be touching the Options, RewriteEngine or RewriteBase directives."
That is, your script that wipes the .htaccess file clean and puts new code in it should not be touching the first three directives. It should not wipe those. It should only wipe and rebuild the actual rules.
Make sure you clear your browser cache before every test. You want to make requests to the server, not pull previous responses from the browser cache.