Problem with menu position module
From your comments, I came to know that you have added a new menu and used it as Menu Block in second sidebar region.

But Menu position module doesn't support new menus.

See the following points from Menu Position module page


  This includes affecting:
  
  
  The main links of the theme
  The secondary links of the theme
  The breadcrumb trail  
  Menu blocks provided by core's Menu module
  Menu blocks provided by the Menu Block module
  


So inorder to work with your new menu, you need to install Menu Block Module.

Menu Position module works well with Menu Block module.

So if you install Menu Block module you can use your custom menus also.


  So… have you ever used the Main and Secondary menu links feature on your theme and wondered “how the hell do I display any menu items deeper than that?”
  
  Well, that’s what this module does. It provides configurable blocks of menu trees starting with any level of any menu. And more!


I've tested this scenario and it works perfect.