The only thing I can spot is that you have created an interlaced 29.97 but have chosen a 30p sequence. Firstly the Skype vid should have been progressive. Is the frame rate on that 29.97 or 30? Either way the video and sequence should match exactly. I see nothing about the sound as 16 bit PCM, 48khz is correct but I suspect there is a .1% drift with picture not matching sequence but FCP may be trying to play the audio at a different rate.