AI OnAI Off
Found the problem. Has something to do with authorization.
Commented out deny users tag and now the missing navigation items are showing. But can't seem to figure out what really is causing it. The the user I have logged in with has all the roles
<authorization>
<allow roles="WebAdmins, Administrators" />
<!--<deny users="*" />-->
</authorization>
Tried adding allow user and it worked but not for roles
<authorization>
<allow roles="WebAdmins, Administrators" users="epiadmin"/>
<deny users="*" />
</authorization>
Solved the third-party plugin specifically GuardDocument was the problem.
Got help from episerver support.
Updated Episerver cms to the latest version and the "CMS" navigation item has disappeared from the dashboard in the back-office and I'm not sure why. I can still manually browse to the CMS using the address bar. The Edit and admin view is missing aswell. Checked modules/_protected and everythings seem to be fine there. Also tried copying the modules/_protected/CMS from another solution but that didn't work either.
Thanks
Adil