Thank you for your post.
I can replicate both problems on both Mac OS X 10.5.8 and Mac OS X 10.6.2. That is,
1. Keyboard shortcuts assigned to commands in the Custom Menu Set Help menu are disabled
2. Trying to assign Command-/ to a keyboard shortcut activates FileMaker Pro Help, even when it is disabled.
Neither problem occurs on Windows.
I have forwarded both problems to our Development and Software Quality Assurance (Testing) departments for review and confirmation. When more information becomes available, I will let you know.