I have a sneaking suspicion I might have a rather simpler answer, by sheer accident. Try creating a new user (Admin) and see if you can recreate the problem. If you can't, you've solved one issue and, in my experience, created another; a user with no files, nothing... I have the same problem so if someone can help with this bit I'd be grateful!
How do I know this? This is the short version... In fairly quick succession I upgraded Filemaker to v12 and OS X from Leopard via Snow Leopard to Lion. Filemaker told me, wrongly, that v12 would only work with Lion (actually it works with Snow Leopard I later found), so I thought as I'm about to lose MobileMe anyway, the writing's on the wall, so get Lion.
Having done all this and converted Filemaker files to the latest version I then found that Filemaker's "send mail" script didn't work - it sends via your default email client or direct SMTP, as you prefer. It wouldn't communicate with Mail. I tried it in v11. Nothing. In v12 at least I got an opaque error message saying:
"Some of the files that are needed are either damaged or have not been installed. Please run the installer to correct this problem."
Which installer? No idea.
Before reinstalling either Filemaker or Lion I put the same Filemaker files on an old iBook G4 (PowerPC, not Intel). The script worked perfectly, ergo it's not Filemaker at fault. I reinstalled Lion. No difference.
I could find nothing on this issue anywhere. Finally I called Filemaker support and having gone through everything either of us could think of the lady I spoke to said, "Have you tried from another user?" No, there's only me.
I created a new (Admin) user, logged out, in, opened Filemaker, ran the script, Mail sprang to life. Solved.
So some preference or permission file somewhere is corrupted (yes, I repaired permissions, made no difference), but which? Now I have a new user who has no access to anything but operates Filemaker's send mail script perfectly!
By the time I got this far Filemaker's support had gone home, so I've no idea what happens next until tomorrow when I'll call again. In the meatime if anyone knows how to resolve the different user problems I'd be delighted to know.
Hope this solves your problem guys. Try it. Good luck.