I'm having the same issue. When outputting 720p/59.94 over firewire to AJ-HD1400 or 1200 there is an audible crackle throughout the program. Its mainly noticeable in fade outs, but not apparent during segments of black/silence.
If I output through the Kona 3 HD-SDI the crackle is not present. This issue was not present two weeks ago and the only explanation I can come up with is the FCP update to version 6.0.6.
Cruising other forums I ran across a couple of people who deleted their FCP preference files and that fixed it for them, however in my situation, that is not the case.
I can output through the Kona tomorrow for the client, but obviously the best way to get this tape for them is to keep it native DVCPRO HD over firewire. Of course, after broadcast it takes a compression hit any way.