Security issue maybe? Did you allow for webdirect in the privilege set of the secondary database?
Are you able to get to the secondary database directly within WebDirect? Even if you have to temporarily allow access, I'd want to prove that the secondary database is really working via WebDirect to eliminate that as the cause.
You say "unable to click" on the buttons in the primary database. Does that mean they do not launch their associate scripts at all, or (as I suspect), the script is running, just not doing anything because the steps that would invoke secondary database simply aren't functioning. How about using the Script Debugger tool (if you have FileMaker Pro) or inserting a Custom Dialogue step temporarily to establish that the script is actually running?