Have you tried going into the script itself and making sure it's set to run script with full access priviledges?
I am having a similar problem. The scripts work through filemaker but not through webdirect. The scripts did work last week. I upgraded the license to include more webdirect connections and things stopped working.
I have checked that the scripts are set to run with full access.
I changed the script from a Quick Find to a normal Find and it's now working. :)