When I go to Preferences/Themes and I choose Custom and check “Show top tool palette”, this is what my screen looks like. The window cannot be changed, it is stuck in this position.
I am using OS X 10.7.5.
Oops, I just found out that OS X 10.7.5 is no longer supported for RhinoMac.
This is a bug in OS X 10.7.5. This does not happen with 10.8.5 and later. The final 10.7.5 version no longer has the “Show top tool palette” option.