I have a discrepancy between my LR Cat and my HDD contents

I have a discrepancy between my LR Cat (54,000+ images) and my HDD content (60,000+ images).
Sync'ed, searched for missing photos and I still have no idea about the discrepancy.
OS X 10.9.4 and LR 5.

Thanks Geoff. do you have '"Do not import suspected duplicates" checked in the Import Menu????' - Yes, I do.

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