From Total Recorder FAQs:
"What is the difference between the recording source settings "Software" and "Sound Board"?
Recording (digital) sound from "Software" and (analog) sound from "Sound Board" are two very different things.
When the recording source is "Software", the path of the sound is:
When the recording source is "Sound Board", the path of the sound (using CD as an example) is:
Recording in "Software Accelerated Recording" mode is similar to recording from "Software" (see the figure above). The difference is that sound does not go to the Sound Board Driver and the Sound Board.
Sometimes you can have fully digital recording even in Sound Board mode. An example would be if both the CD drive and the sound board have digital connectors and are connected with a digital audio cable. "
Bottom line: apparently enables ripping of streams that are not recordable in other programs. Disadvantage: only .wav and mp3 ripping/encoding are available, though once you've ripped the .wav you can always convert to APE in MJ. Also can adjust settings for proper bitrate and frequency. Its worked like a charm for me.
HTH