MacBook Pro LED light flashing
I'm assuming you're talking of the camera status indicator LED. If it turns on for a svery short time, it means that some program tried to access the camera. From your description this is likely Skype.

As far as I remember there was a problem similar to this in an earlier version of Skype where it repeatedly tried to initialize the camera. Update your Skype to ensure this is not the case.

If that doesn't help, then check the camera settings in Skype. For example try not selecting your built-in camera as a video source in Skype at all. If that cures the flashing light, you know that the cause is Skype.