I have the same problem using both FM 7 and 8.5 on 10.4.8. My Option and Command keys do work in all applications including Filemaker. However these two functions do not work in Filemaker:
1. Option-Drag to duplicate a field
2. Command-select to select multiple objects.
These are very useful features and I wish they worked. If anyone figures out this problem please post the solution! I submitted a trouble ticket to FileMaker and hopefully they will respond.