If it helps any, I have been tinkering with /wp-admin/option-permalink.php again and noticed if I comment out:
$wp_rewrite->flush_rules(); on line 90 or so, it does not prompt me to download option-permalink.php.
And then of course, commenting out that:
if ( ! got_mod_rewrite() )
$prefix = ‘/index.php’;
Allows it to display fully.
And a final note… and this is perhaps the scariest part. It works *seemingly* flawlessly! Come on WordPress gurus, tell me what’s going on in those two code areas, please.
I feel like I have fixed my own car trouble, yet I have tons of parts leftover.