How many pages are you trying to apply it to? You can always apply it to one page at a time with the server behaviors panel. Just open the pages that you want restricted and go to server behaviors and apply the "Restrict Access to Page" server behavior.
The page manager is just supposed to do that for you by opening each page and applying it for you and make it less repetitive, but worst case scenario it can be done individually.
I could try to debug it.... it may have something to do with a page name or something else with your site definition. If you give me FTP access I could download the site and try it myself. I need to reproduce an issue to fix it, so maybe see if it is a particular page that is causing the issue by applying to just one page and see if the problem still occurs... try a couple of different pages to be sure. If you narrow down a page I might be able to look at that page and diagnose it from that.