Here’s how I fixed it. I made a mod_rewrite condition (RewriteCond) that excluded any Feedburner user agent (thankfully that was intact and correct). So my rewrites to force all traffic through my SSL site EXCEPT for Feedburner’s queries is:
RewriteCond %{HTTPS} off
RewriteCond %{HTTP_USER_AGENT} !^FeedBurner
RewriteRule (.*) https://www.site.com%{REQUEST_URI}
So there we go, that has solved ALL of my FeedBurner problems.
Disregard. I just added an @ in front of that function.