We have noticed a serious Lip Sync problem. I edit the AMA Supercross for CBS & Speed Channel on location. We kept getting lip sysnc problems, either on the feed to the network, or feeding packages to the main truck. We master 720 59.94 Prores with 5.1 + 2 Surround audio.
The audio would be in sync on the computer monitors and thru the Graham-Patten Sonarae system. The audio output on the KONA 3 would drift substantially. The cure we found was to make sure there were no gaps on the video track. All gaps must be filled with a slug.
Ours systems are
2 3.2 ghz quad with 8 gig of ram
Rourke Data 24 TB Raid with Fibre Jet networking
Graham-Patten Sonarae Surround Sound Monitoring
You can see the complete system at locationedit.com
Vide-Post / San Diego
Dual 2.5 G5
3 Gig Ram
Medea 2TB Fibre Raid
Medea 640 gig SCSI
Did you try and render you audio as a mix down first? In fcp mixdown does not mean what it typically means, but rather it renders all audio to designated tracks as one temporary file. It helps with rt and multiple audio channels.
Select all and command-option-r in the timeline. It won't hurt your 5.1 + stereo.
I have encountered a similar problem, although it seems to be that the video out of the Kona SDI output feeding my baseband monitor lags the video and audio in the sequence. The audio out of the Kona AES output feeding my speakers seems in sync with FCP, but appears out of sync with the program monitor, i.e. it is slightly ahead of the monitors video. Is this the same as what you experienced? I have not tried the slug workaround yet but will.