If you are using an advanced layout you'll need to ensure that they are listed in the layout.html file. When using an Advanced Layout you have to manually place the menus where you want them and call them by their PHP Tags Chops has defined.
<!-- System:Calendar -->
<!-- System:Menu:Guides --> (if Guides is the name)
<!-- System:Menu:Links --> (if Links is the name)
<!-- System:Menu:xyz --> where xyz = the name of any custom menu you have built. All custom menus get called in this format.
If you are not using advanced layout then you'll want to look at the following 2 admin menus and ensure that they are checked and placed in the order you want them to appear.
Basic Menu Administration
Menu Category Placement and Order
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Six Demon BagJack Burton: Hey, what more can a guy ask for?
Egg Shen: Oh, a six-demon bag!
Jack Burton: Terrific, a six-demon bag. Sensational. What's in it, Egg?
Egg Shen: Wind, fire, all that kind of thing!