random broken permissions? playing with my auto nav?

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I've been running into random issues with permissions not following the correct parent page. (Very Randomly)

lets say I have

Home
-Cookies
+Milk

Cookies is set to (Manual)
Milk is set to (By Area of Site)

On a bad page Milk will not follow Cookies but Home.

Usually after making a copy of the parent with Children I am able to correct the issue. (annoying but i can usually get it to work correctly)

recently:
I've been playing the auto-nav and I'm noticing some crazy stuff that is similar to my permissions error only its showing the links under the wrong parent

I have
Home
-FAQ
-Class_Test
+ClassName
+ClassChat
+ClassCritique

In navigation I will get things like (attached image *notice no arrow on top button// using ambient add-on but same thing happens with the default auto-nav\\)
FAQ->classname,classchat,classcritique

these pages are children to another parent that is not a child of FAQ

it seems like every time I log-in I get the same issues but with different pages, when I clear the cache it usually doesn't change anything. I usually have to manually copy or rebuild the page. Can't figure out what would cause this.

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SheldonB