Still very strange. Shouldn't the calls be encrypted? If the other call was started before, and the OP's client wasn't there for the handshake, how could it decrypt the call content?
Calls Skype to Skype are encripted, but as far as I know you lose that when you make calls to landlines or mobiles.
The spy /monitoring software can be running at your computer --thing that is usual-- (so before encrypting...)
They don't need to broke any encryption ("NSA style"), only a "bug on windows"...