Do you know what version of Apache you are running? What version of mod_rewrite? Do you have all of the other Apache modules that NNF uses in its `.htaccess`? Does anything jump up in the Apache logs?
Honestly, if without the `IfModule` the rewriting doesn’t work (more specifically, lines 169 to 172 [1]) I am not sure how you are going to make friendly URLs work by writing your own `RewriteRule`s. Either Apache applies RewriteRules or it doesn’t. Though I am confused about how it would be able to apply the HTTPS rewrite if that were the case.
That said, this seems to be a real edge-case with your hosting setup.