I'm running plogger since yesterday, and everything was working fine (including cruft-free urls), but when I turned on the comment function they stopped working. I now get an infinite redirect loop :(
I tried deleting the .htaccess file, and then recreating it by turning on the option cruft-free urls again, but that didn't work..
I solved it.. apparently when you enable comments the .htaccess file gets rewritten, which changes the RewriteBase value to "/". Since I run plogger in a subdirectory I need to have a different path.. So I changed the path in plog-admin-functions.php and now it works :)