You're right; your problem is coming from the fact that PDF generation isn't server-side compatible. The typical solution to this issue is to run a robot (either a separate instance of FileMaker client on the server or a separate client machine) and do it from there. Another option is using web tools to generate the PDF.
Here are some related threads that discuss the issue.
Thanks! I will look through these and find the least painful way to skin this cat. It beats banging my head on my desk repeatedly!