ManicInfinity hmmm never saw it, but it looks like it creates a pop-up for the user:
ACS.Web.Email.MailboxForward.Business.MailboxForwardBLL.GetUsersUsingCertificate() in C:\Projects\ACS.Web.Email.MailboxForward\ACS.Web.Email.MailboxForward.Business\MailboxForwardBLL.cs:154
ACS.Web.Email.MailboxForward.Default.Page_Load(Object sender, EventArgs e) in C:\Projects\ACS.Web.Email.MailboxForward\ACS.Web.Email.MailboxForward\Default.aspx.cs:65
With an ASPX file.
When you run all this in a script, do you get any login pop-up? Maybe the previous command didn't log correctly, or it is a perticularity of V2 Cmdlets, can you try with a classic Get-Mailbox?
I never used the certificates to log in, always with login / password (stored safely as Secure String and decoded in another DLL), so there might be a behavior here.