If you are using ordinary analog line out to Minidisc in (stereo minijack - stereo minijack), my guess is that you're using the MD's microphone input. If it has a line input use that; if it doesn't have a line input you've got a problem, but an attenuator to reduce the level by about 30 dB should do the trick.

If your MD has optical input (likely if it's Sony) and your sound card has optical output (only a few do), doing it digitally is a good plan, using that optical cable they tried to sell you.

Anahata