Audio won't follow in- point  when exporting from Final Cut Pro

I am using Final cut Studio 2 on a Brand new mac pro which is connected to a an AJA IO pro box (not IO HD). If I set an in point on a time-line in Final Cut pro and send it to Compressor, only the video uses the in point. The audio starts from the beginning of the time-line. This is a huge annoyance and something I used all the time on my G5.
Does anyone have any ideas?
Thanks in advance for your help.

Yea that worked. I was mostly trying to debug it for my client today, since they have the same system I do, minus the AJA and I have no problems sending to compressor with or without marks. Is this a "known" bug or is something with the AJA setup?

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