I have done some work in trying to get Basilisk II to run in 64-bit mode on Mac OS X and I have noticed some calls are to functions not available in 64-bit mode.
Attached is a patch that uses SetSystemUIMode instead of ShowMenuBar and HideMenuBar, the latter two not being available for 64-bit apps.
Also, the Clipboard functions are deprecated and not available for 64-bit apps.
patch to use SetSystemUIMode