That portion appears to be fine. I see that on my test installation too.
127.0.0.1 - - [18/Oct/2009:23:14:47 +1100] [127.0.0.1/sid#7fea72ee8860][rid#7fea732d3bd8/initial/redir#1] (3) [perdir /var/www/_silverstripe/] applying pattern '.*' to uri 'sapphire/main.php'
127.0.0.1 - - [18/Oct/2009:23:14:47 +1100] [127.0.0.1/sid#7fea72ee8860][rid#7fea732d3bd8/initial/redir#1] (4) [perdir /var/www/_silverstripe/] RewriteCond: input='/_silverstripe/sapphire/main.php' pattern='^(.*)$' => matched
127.0.0.1 - - [18/Oct/2009:23:14:47 +1100] [127.0.0.1/sid#7fea72ee8860][rid#7fea732d3bd8/initial/redir#1] (4) [perdir /var/www/_silverstripe/] RewriteCond: input='/var/www/_silverstripe/sapphire/main.php' pattern='!-f' => not-matched
127.0.0.1 - - [18/Oct/2009:23:14:47 +1100] [127.0.0.1/sid#7fea72ee8860][rid#7fea732d3bd8/initial/redir#1] (1) [perdir /var/www/_silverstripe/] pass through /var/www/_silverstripe/sapphire/main.php
Looking at that test, its checking to see if main.php is not a regular file, which correctly should return false.