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Make sure that the CF card has been cleaned before you use it with WinUAE. We've seen occasions where WinUAE uses a partition on the CF card as harddrive instead of the whole CF card. Of course the real Amiga cannot see the Amiga data if it does not begin in the beginning of the CF card.
Also run HDToolbox on the real Amiga to check if the CF card is actually recognised as a harddrive. There are CF cards which fail to identify themselves to the IDE driver.
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