I think perhaps all ATRAC-based stuff is blocked from being transferred, only LPCM WAV can do that. I seem to recall reading this in the manual a while ago but I can't seem to find it when I looked today.
There is a setting deep in there to switch the output from headphone/line out, you want line out to do this kind of a transfer, then hook up to your soundcard (preferred M-Audio Audiophile2496 for about $120CDN) and record in real time.
Did you try it in LPCM WAV mode yet? that way you just open SonicStage (has to be 3.2 or higher) then connect the Hi-MD and a window appears on the right with the new recording in a folder called "Unnamed". I highlight that folder, press the arrow in the middle pointing from right to left (from md>computer), it says "do you want to do this blah blah" I click yes, then wait a long time. It transfers the whole file from the disc encrypted in OGM format or some extension then it makes a WAV version which you can work with.
Also very very important (during recording only) is to turn off the autogain everytime you insert a new disc, and set the rec levels manually. Check over here:
http://forums.minidisc.org/index.php?showtopic=9045
ps congrats on the Hi-MD, which one did you get? I've got MZ-NH1
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