lucy24 - 9:27 pm on Apr 4, 2012 (gmt 0)

I have redirects and rewrite rules in multiple htaccess files throughout different directories. The redirect rules work but I can't get the rewrites to work outside of the root level htaccess. <snip> [R=301,L]

That's not a Rewrite, it's a Redirect. When you say you have both, do you mean that you have both
RewriteRule blahblah [L]
and
RewriteRule blahblah [R=301,L]

or do you mean you have both
RewriteRule blahblah
and
Redirect 301 blahblah

If it's the second, prepare for a chorus of Danger! Danger!