For .ape to .mp3 transcoding the convert.conf file specifies [faad] as Monkeys Audio decoder, this should be [mac].

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brand@silver$ diff -c convert.conf.sample convert.conf
*** convert.conf.sample Mon Apr 12 23:26:34 2010
--- convert.conf        Tue Oct 26 18:12:03 2010
***************
*** 127,133 ****
  
  ape mp3 * *
        # FB:{BITRATE=-B %B}D:{RESAMPLE=--resample %D}
!       [faad] -q -w -f 1 $FILE$ | [lame] --silent -q $QUALITY$ $RESAMPLE$ -v $BITRATE$ - -
  
  wvp mp3 * *
        # FB:{BITRATE=-B %B}T:{START=--skip=%t}U:{END=--until=%v}D:{RESAMPLE=--resample %D}
--- 127,133 ----
  
  ape mp3 * *
        # FB:{BITRATE=-B %B}D:{RESAMPLE=--resample %D}
!       [mac] $FILE$ - -d | [lame] --silent -q $QUALITY$ $RESAMPLE$ -v $BITRATE$ - -
  
  wvp mp3 * *
        # FB:{BITRATE=-B %B}T:{START=--skip=%t}U:{END=--until=%v}D:{RESAMPLE=--resample %D}