This is the nature of Firewire Output. FCP does the same thing - so the key is, when monitoring audio, pick with monitor you want to use, and listen to the audio out put from that (e.g. if you are looking at the NTSC montior, listen to the audio coming off your deck).
In Engineering, we do not like this sync problem either, in fact we had this disabled in early builds of Media 100 Producer. Beta testers informed us that they would rather have monitoring on then not on, so we turned monitoring on even though it is out of sync.