Hi @Sam Aly
According to my research, I found a similar question here: Problem with WinRM on Exchange 2013 Management Shell and Exchange Toolbox on a new exchange 2013 with CAFE and BE on single server installation
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This is how I went about diagnosing this, with the first Exchange Server 2013 installed and running, I installed a second Exchange 2013 Server with only the Mailbox server role.
On the second Exchange Mailbox server I was able to access the EMS and the Exchange Toolbox successfully.
Now from here on it's simple I only have to do a comparison of the Powershell settings in IIS Manager on these two Exchange servers.
Internet Information Services (IIS) Manager, Sites, Default Web Site, PowerShell and in the Actions Pane, choose Basic setting, physical Paths - on exchSvr1 has C:\Program Files\Microsoft\Exchange Server\V15\FrontEnd\HttpProxy\PowerShell while C:\Program Files\Microsoft\Exchange Server\V15\ClientAccess\PowerShell on exchSvr1 changed the physical path to C:\Program Files\Microsoft\Exchange Server\V15\ClientAccess\PowerShell
After changing all these I did an IISReset on the exchSvr1 (the affected server) and tried the EMS and Exchange Toolbox, they all worked.
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