The development team at Media 100 has not been able to reproduce the audio sysc programs you describe. Could you please email me a description of your setup and any other relevant information.
For example: video standard, audio frequency that you are recording to disk, audio input source (embedded/AES), is the problem only observed with the XDcam deck, is audio leading are trailing the video, did the acquire panel show any loss of signal (yellow lights) prior to the start of recording?
My email address is MHouskeeper@Media100.com
Marshall Houskeeper
Media 100 Software Development