Similar problems here. Seems to have started with Leopard installation.
The main menubar of Motion only shows the Apple; other items — File, Edit, etc. — are missing.
Most drop-down menus will not drop down. Same problem is happening in DVD Studio Pro.
I’m running Final Cut Suite 2, which had been working fine. I just re-installed the entire suite; the problems are still there.
Following other folks suggestions, I’ve tried repairing permissions, turning off Spaces, unchecking everything in Spotlight preferences, logged on as a different user, and more.
I’m glad I’m not the only one!
Les