Could you please check what LDMS version you are currently running for both core server and client server? Also whether you have updated the definitions to the latest status?
In LDMS 9.5 SP1 with latest definition updated, skype.exe is not detected as virus in my environment.
We are using Scan Engine 22.214.171.124 with virus definitions dated 9/22/2013.
Land Desk is version 126.96.36.199
I saw the same with Skype version 188.8.131.52, to avoid any loss of time I updated all clients to the latest version of Skype.
With the latest version skype.exe is clean.