This will get you on the newest header block, it might now fix the problem though since it could be deeper rooted then this.
You can also take a look in the getStoreCategories method of the helper: Mage_Catalog_Helper_Category As this should be what is creating the category tree used for your top navigation.
I would properly look into this before changing the tempalte.
If you want to go ahead and try replacing the old top menu renderer, you can go about it this way: Depending on what template you are extending from, go look for the page.xml file in that. Find the block with the name: catalog.topnav, it should look something like this:
<block type="page/html_topmenu" name="catalog.topnav" template="page/html/topmenu.phtml"> <block type="page/html_topmenu_renderer" name="catalog.topnav.renderer" template="page/html/topmenu/renderer.phtml"/> </block>
Go to your templates local.xml file, and place this in the default handle, and place it in the reference pointing to the node wrapper you want to place your navigation in (Properly header).
You should also remove the block currently rendering the header. which in your template would have the type catalog/navigation.
Thank you very much i had the same issue and solved it by going to system > configuration > catalog > Category top navigation and set the value 600 its not a fixed value i just added maximum number and all sub and sub of sub are shoing fine i hope this might help you too
regards
There is another option in System->Configuration->SW Extension->Magamenu and find option "Display empty categories" which is sometimes Selected as "No" and select as "Yes" and you are done.
If you don't need a general solution, a quick CSS solution which will work only for that specific menu is:
.header-nav-container-home ul.nav-menu li.nav-5-1 ul li.parent:hover ul { left: -100%; }
Add this line at the end of menu.css.
Thanks. This did it for me
thanks this method is working i am blogger at : Massager Consult