It's hard to make a plunkr example, but it's easy to reproduce.

As I have a SPA I do authentication serverside through $http (webAPI). I create a $http method which calls a login functions on my backend server, this will set a cookie to authenticate.

After $http is complete I check my cookies:

public get isAuthenticated(): boolean
{
    var cookie1: string = $cookie['.ASPXAUTH'];
    var cookie2: string = $cookie['.ASPXAUTH_USERID'];

    console.log(cookie1, cookie2);
    console.log(document.cookie);

    if (cookie1 && cookie2)
    {
        return true;
    }
    return false;
}

Odd part is that the variables cookie1 and cookie2 are empty, but document.cookie contains the newly set cookies.

After a page refresh all is fine, it seems that $cookie doesn't recognize cookies after they have been set by an ajax call.