>> Check your configuration in MusE Settings->Global Settings, check that
>> the arranger is set as a MDI-subwindow as I expect that is what you
>> want.

>> That moved the arrangement back into the parent window, however, now
>> I only get the menu strip that contains "Edit|Functions|Window Config",
>> and not the one that contains "File|Edit|View|Search|Tools|Documents|Help".

>Oh, I didn't really try to use it as my machine with ubuntu isn't really usable for music but I'll try to verify this tomorrow if time permits.
 
This seems to be fixed in the final release of Ubuntu 12.04, I get the expected context menus now.