You need to make sure that the Apple Loops you add to your ~/Library/Eigenlabs/Loops directory have the file extension '.aif' or '.aiff' at the end, e.g. 'Loop1.aiff' or 'Loop2.aif'. If it has any other extension, e.g. Loop3.wav, it will not appear in the EigenD software.
Please Note: We do NOT support .aifc files in our Apple Loop player.