I am having a similar problem with an 8-core Mac Pro (MacPro 3,1) – no external hardware other than a DVCAM deck, no expansion cards or drivers.
Audio slips significantly over even a 5 minute clip when I import audio from a separate sound recorder (at 48/24).
If I open the same clips on my MacBook Pro – using FCP’s default settings – I don’t have the issue at all.
I have tried setting the Default Sequence to ProRes 422 1280x720p (closest I can find to match video settings of the camera) but it doesn’t seem to help on the MacPro, whereas the laptop seems happy, whatever I throw at it.
Any advice very welcome.