All of the Mac users in my organisation get put on mute whenever they make or receive Skype calls. None of the Windows users are affected. It mutes their microphones (headset or built-in) when their outgoing call is connected, but if you add a second call to that they stay off mute.
Their microphones are similarly muted whenever they answer a Skype call, whether or not it's a group call.
We're on Skype 16.3.240 right now, but it's been the case for a few months now.
Best Answer
Seems to have been fixed in the latest patch from Microsoft.