Looks like the site note plugin gets lost around when I activate Advanced Access Manager plugin. Something with the user roles conflict, I don't really know, I am new at this whole PHP thing :p
Ok, here is what I did to get the site notes to work again:
Edit file class.DSNManager.php in the site note plugin directory, edit line 223 from:
$editable_roles = apply_filters('editable_roles', $all_roles);
$editable_roles = apply_filters('all_roles', $all_roles);
This will show the Super Admin in Site Notes Configuration under Settings. Once I was able to select that, the menu "Site Notes" appeared and I am able to use it now.
I am not sure if that is the right fix for the problem but it works for me, and I hope the developer can look in to it and do the proper fix :p
Hope this helps someone :)