I've just purchased and installed the latest version of BulletProof Security Pro and have it running on a Multisite 3.3.1 installation successfully.
When we upload a file using the Media uploader the process freezes at 100% and displays the following message:
Only Super Admins can access BPS Pro15645
See a screenshot here.
The file uploads OK, and we are able to edit the metadata in the Media Library so this isn't a show stopper, but it does appear to be a bug specific to the plugin (I think).
Thanks again for taking to time to put this plugin together, I'm incredibly excited to continue using the Pro version!