I also have a missing menu bar in linux. I'm using Ubuntu 12.04, x86_64, Gnome classic (no effects), with a standard theme (ambiance). Bible analyzer is version 4.6.10, but I had 4.5.5 previously.
Untill I saw this topic, I wasn't aware there was a menu bar.
I just installed in 12.04 32 bit, running in virtualbox, with xfce4 as the DM, and I have a menu bar there.
Does the menubar have any dependancies on the display setting used?
strace shows that the menu is being opened.
open("/opt/bibleanalyzer/mainMenu.py", O_RDONLY) = 3
open("/opt/bibleanalyzer/mainMenu.pyc", O_RDONLY) = 4
Also, 4,5,5 has been completely removed, and configuration files cleared and rebuilt.