Hello all, hoping that someone can help.
I'm using MobileJoomla 1.2.5.1 on Joomla 3.0 and all is working great except for the creation of a separate mobile menu. I previously installed and created a mobile menu on a Joomla 2.5 site and it worked fine, but repeating the same process and spending hours inspecting and comparing the two setups has left me stumped. The Joomla 3.0 setup will only recognize the sites main menu.
Next issue is the ScientiaMobile plugin. Again, it works fine with Joomla 2.5, but throws a server error on 3.0.
Anyone experienced and/or has a solution for these things?
Thanks for reading.

How do you create separate menu?

Issue with ScientiaMobile plugins is fixed, reinstall MJ to download&install latest ScientiaMobile plugin.

With Joomla 3.0 there is no option to copy a menu. I created a new menu and followed the rest of the instructions found here:www.mobilejoomla.com/documentation/12-getting-started/56-creating-mobile-menus.html and batch-copied the menu items into the new menu. I also tried simply creating a new menu item, but either way the only menu that will appear on mobile in the default desktop site menu.
As for the ScientiaMobile plugin, I uninstalled and reinstalled MobileJoomla today, but the issue seems to remain and I need to disable the plugin to avoid the server error. I will try again though in case I missed something.
Thanks for helping, I appreciate it.

Uninstalled, downloaded and installed latest version, (confirmed I already had latest version, but just in case there was a corruption), activated and unfortunately no change. No access to separate mobile menu and the ScientiaMobile plugin throws a 500 error if activated.Again, Joomla 2.5 seems to work as intended, but there appears to be some conflicts with Joomla 3.0. I'm hopeful to resolve this, as I feel you have a great product here. Thanks.

1. The best way to create mobile menu is to add necessary items as aliases ("System Links/Menu Item Alias") to desktop items (unless you need items specific to mobile mode).

2. Update MJ again, Scientia package is fixed.

Uninstalled/reinstalled and I confirm Scientia package is fixed with no 500 error. Thank you.
As for the menu, yes I'm needing different items to display on mobile devices. (The items will be displaying cross-platform for each device. Only a need for one mobile menu.) I'm not seeing anyone post this issue, so I suppose I may have misunderstood or missed a step somewhere. The only instructions I've found for how to accomplish this appear to be for Joomla 1.5. Do you suppose the fact that I'm creating a new menu without copying an existing one might be an issue? No other known way to do it with Joomla 3.0, as you can only batch process menu items to an already existing menu.

I'm also using Joomla 3.0.2 and the MJ 1.2
7 and I'm horrified to say the menu issue it has has rendered MJ unusable in Joomla 3.x

I have joomla 2.7 where MJ works great but in my first Joomla 3.x, the menu system has become unpredictable. I have done thr following;

1. created a mobile menu for MJ as in the tutorial on this site
2. Tried associating menu items with mobile templates
3. Tried forcing the homepage in general tab. This leads to all menu items showing the default link.

Despite all these, I display a page containing only the menu and no content and other times, only a few menu items show content while the others don't .

Does anyone have any ideas because I've tried pretty much all the tricks in forums to no success.

Hey lesanjo, this may be of some use to you and to others who may be struggling with it. I ended up getting the separate mobile menu working in Joomla 3. Here is my setup and how I did it:
I'm using my own responsive template as a separate mobile template with MobileJoomla. It shares all of the same module positions as my desktop template. 
1. You don't have to copy any menu. I think a lot of people are getting confused on this part, but it's really not a necessary step. Simply create a new menu and name it what you want. (ie: Site-Mobile-Menu). 
2. Once you've created the menu, create a module for it (I suggest naming the module the same as the menu), and assign the module to the same position as the menu you want to replace. (In my case, I'm replacing the Main Menu located in position-1). Save and Close.
3. Still in Module Manager, open Mobile Menu (located in position mj_all_header). Under options you'll see it's assigned to Main Menu by default. Change that to the name of the new menu you just created.
4. Open up MobileJoomla component, make sure you've selected your correct template for each device, click on Advanced Settings, then click on Modules. You'll see the list of all modules, find the module for your new menu and deactivate it for Desktop, leave activated for all mobile devices. Now find the module for your desktop menu (if you did it right it should be in the same position as your new menu), deactivate the module for all mobile devices and leave activated for Desktop only. Save your changes.
5. Add any menu items you like into your new menu. If you have items that will point to the same pages as your desktop site, make sure to use Menu Item Alias under System Links to point to the correct page.
6. Check out your site on mobile and you should now see the correct menu. 
Now, as for Forcing Homepage, you are right about that. It doesn't work correctly for me either. It will load the correct homepage that I direct it too, but for whatever reason it locks and redirects all links to the homepage. Not good. As a work-around, I'm using the Mobile Content plugin on my default desktop homepage (which is currently doubling as my mobile homepage), and simply wrapping {desktop} and {mobile} tags around the appropriate content.
I hope that I've helped with this info. Oh and BTW, I tried responding to this earlier from Firefox, but this site is displaying the mobile version in Firefox desktop? Weird. I'm now using Chrome to write this and all is well.
Take care.