What could be causing a VERY strange audio lag?

Hi,
This is a problem that I have begun experiencing in the last week or so and I have found a post on another site of someone who is having the same problem. I'm not sure if it is an update gone wrong but it is nothing I have never seen before in my years of video editing.
Ok here's what's happening...
If there are two audio tracks (say a stereo music track), when I push play one tracks runs slower than the other. However this is where it gets interesting... One thing I observed (very noticeable with headphones on) is that if it is the left channel which is running slow, when you pause the video and push play again, the right channel then becomes the channel which runs slow. It swaps channels every time you pause and play. With the slow channel, there is also a good half a second delay before it starts after the good channel (and vision) has begun. So if you are listening to music, it will start in the left channel then the right one will come in slower about a half a second later. Then you push space (pause) then space (play) and the same happens but it starts in the right channel.
The computer I have is very powerful and all my hard-drives are internal so I can't see it being a system issue. I also only reinstalled my computer fully a few weeks ago so I know that junk on my computer isn't the issue either. As from other checks, it also happens in other projects, even older ones which I had finished ages ago and never had any problems. The problem actually went away earlier this week but has just come back so it seems to be an intermittent problem.
Very strange... Any ideas or assistance would be great as I have come to a bit of a standstill with this.
Matt

Hi,
Here's the answers:
Where did the audio come from? I have tried a few various methods which all have the same result including bringing in a stereo 48KHZ aif or using footage captured from the tape (stereo only - the problem goes away if they are changed to two discrete mono channels)
How was it copied to the computer and imported to FCP? Either captured in the case of footage from the camera or from an AIF file where it would be dropped into a bin and then onto the timeline.
What format is the audio in? Sample rate? Everything is at 48KHZ.
What kind of sequence are you working in? I only use two types of sequences and it happens on both being HDV - 1080i50 and DVPAL 48KHz Anamorphic.
Is the audio's format native to your sequence settings? Yes, both for the captured footage and the imported audio.
Hope this helps

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