When I installed Mobile Joomla, 4 templates were created automatically (mobile_iphone, mobile_imode, mobile_pda, mobile_wap).  The issue i'm having so much trouble with, is that I can ONLY see the modules under "-Select Template-" of the drop down, not in my actual PC template.
The modules that have "Pages" set to "All" is displaying on the PC template, but not the ones with "Varies". This is causing major issues as the modules no longer display on the PC site, and I cannot figure out how to assign each of my modules to the PC template, and then how to copy them in the mobile_pda template when I'm ready.   
Your help is appreciated.  I cannot attach a screen shot or any file for some reason to this ticket. Let me know if you need one.

1. What Joomla version do you use?
2. Try to disable "Mobile-TeraWURFL" plugin and clear cookies. Is the problem still there?

1. I use Joomla 1.5.15.
2. I already tried disabling Mobile-TeraWURFL plugin with no luck. As well as cleared my cookies.

I actually uninstalled Joomla Mobile and restored my Joomla site to how it was. Most of the issues came from the newly created Mobile Menu that was disabling sub-menus and modules from displaying anywhere on the site if not selected in the Menu Selection.

Yes, Mobile Menu module modified menu object, but it shouldn't affect desktop version of a site. And note that this issue will be fixed in 1.0RC2 (approx. release date: 16 of August).

oh wow.. so in few days this issue will be fixed. I am glad you're aware of the issue now. Let me know if you need any more details. Can you please post me when this issue is fixed?

The issue was fixed in few days after release (just after it was firstly detected). The patch is here: github.com/mobilejoomla/mobilejoomla/commit/82cf21939251dae8ff2276a35a296836abc187f8