This is very common issue and usually generate template break or module not appear like expected.
When you create new section, you SHOULD create a menu item point to that section:
[Joomla 1.5]
[Joomla 1.0]
When navigate to that section, categories, or items of that section, Joomla! will looking for the menu item link to it and assign its id to Itemid. If not found any menu item, Joomla! 1.0 will assign Itemid=1 and Joomla! 1.5 will take the current Itemid. That will make Joomla! 1.0 think it’s still in Home, and Joomla! 1.5 stay in current location.
So I strongly recommended that if you create new section, you should create a menu item point to that section. That menu item can be place in any menu (display or not display) but must be PUBLISHED.