Sample Rates not Matching

I'm using Firewire from my Sony HVR M15U to FCP 6. After ever capture I'm getting a message "that 1 or more of the media files does not match the sample rate of your source tape". It also warns that audio may be out of sync with video. However, that does not seem to be the case. I have check the sample rates and they seem to match. Any thoughts?

I saw this warning several times at a station I was freelancing at several months ago. Never could figure out the difference it was seeing. Never made a difference with sync or anything else.
I might have noticed a longer render time with those jobs that had the warning, but that is just something I thought I noticed and I never had time to set up a test of that.
All jobs output to tape just fine in the end. Happy me, happy client.
They were using a Blackmagic card for input if that could be a control variable. Sorry, I don't recall the model number.

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