Make sure your settings in the Kona Control Panel are the same as your monitor native resolution – no resolution converting allowed. Jeremy Garchow figured this one out a while ago.
I have an 4:3 NTSC broadcast monitor and converting will always give me pops when I switch aps. If the Kona Control Panel is set to Primary Native Format 525i 29.97 there are no audio issues.
I only have problems when I am switching between AE and other programs, if I am staying in FCP I can leave the Kona in whatever format I like and there are no problems. Only when I hop around to different programs do I get the pops and clicks and pauses and dropouts…broken record.
I have contacted AJA about this three times with no response from them. The cow is way better for support than AJA.
MacPro Dual Core 2 Duo 3.0Ghz, 6GB ram, 1TB Raid, Tiger 10.4.11, FCPStudio 2