Hi Johanus,
Both LAN Speed Test and LST Server support Server 2012 R2. I use both on my Server 2012 R2 machines all the time. Do you have an anti-virus engine running on your server 2012 that might be causing issues with the testing? What happens if you temporarily disable it and try testing? Also, if you manually copy a bigger file from a workstation to this server, is it noticeably slow?
-Pete
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