Rob,
I had the same issues after removing Perian.
You might just have to bite the bullet and do a reinstall.
I zeroed my drive & reinstalled 10.5 & fcp.
Now it works fine (I made sure not to install Perian).
One other thing to look out for in 10.5.6 (for me) is that transcoding a file over 4 minutes using esata would always fail. The same drives using firewire or usb2 had no problems.
-good luck