Most likely you have a DSO Server and will need to do additional BPS setup steps to make the secure.htaccess file readable/writable.
You can check if you have a DSO Server by going to the BPS System Info page and checking these things below. The Server API will either say CGI or DSO.
Server Type:
Operating System:
WP Filesystem API Method:
Server API:
If your Server API is DSO then click the link below.
DSO Server Setup Steps
http://forum.ait-pro.com/forums/topic/dso-setup-steps/