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Conclusion: Windows Server 2003 and EMM did not work so good.
Installed on a Windows Server 2008 with the same IP and hostname and did not configure any FW settings, worked just fine.
Still think there was a .NET issue. If I had time I would try to install .NET 3.5 SP1 and then try to install the EMM Proxy on the Windows Server 2003.
I tought EMM did check the .NET version.