Just came across this Thread in my WP Tag travels.
I have BPS and WP Super Cache with mod_rewrite working perfectly well together on a testing site, but I had to use the BPS Custom Code feature to combine the .htaccess code in order for everybody to be happy. ;) The WP Super Cache htaccess code should come before the BPS .htaccess code as shown in this working .htaccess file in the link below.
The htaccess file is posted here: http://forum.ait-pro.com/forums/topic/where-is-the-log/