It's close to impossible to support FPX any longer, because Microsoft no longer supports it. In fact they've told the company they hired to create FPX for Linux/Unix to no longer distribute it.
Do you have it installed for any domains that work? If so, check to see the rights and permisions for the various folders in a working directory tree.
I've just checked the /usr/local/directadmin/scripts/frontpage.sh script and it doesn't seem to have anything which would fix the problem.
You might want to try rebuilding httpd in customapache; that could fix frontpage issues.
Jeff