Here's an animation of the problem, which I'll explain below:

Frames:
1. Menutree and menu are on the same page (initial state)
2. Hover over Tab 1 in the menu and it overlays the root nodes of the menutree just fine
3. Open up one of the nodes
4. Hover over the menu again and notice that the root node in the menutree "Tab 1" does not show up, however the text "Menu 1.x" all show up *BUG*
5. Hover over to a menu right next to the one we just highlighted and notice that the bug is fixed
6. Hover back to the menu that had the bug and again it's fixed
Conclusion: it seems like the menu does have the code to internally change the Z-order or do whatever it does, but that code seems to be executed in the wrong place in the code (or maybe it's the right place, but a similar call should be made in another place as well).
Not having an easily readable mmenudom.js file, I don't want to mess with the JS within that file, so hopefully somebody here can help me either create a work-around or fix this bug. Since the menu [probably] wasn't originally designed to also be used as a tree control, I understand why a "submenu" would show up, while the main menu would be hidden. I just wish the same style could be applied to the sub-menu's.
I hope my explanation made sense. Please let me know if you need any other information from me to help solve this problem.
Thank you,
Boris
P.S. Off topic: Does this site allow local hosting? Our firewall blocks any image hosting sites and in case this information will be archived, I will not keep the images forever on my personal site.