all depends on your crackle, your sound card, the drivers of your sound card, the speed of your pc, amount of ram, speed and defragmentation status of your hard disk, whether you are using the right sampling frequency...

are you sure you are not overloading the audio through the line in and clipping? Either overload on the sound card input through the mixer slider level being too high, or clipping on the minidisk player due to the minidisk volume being too high into the line input of the sound card. If not clipping, you might just need better hardware.

try the windows sound recorder instead of cubase for an experiment?

if you play the wave file through media player instead of cubase, is the crackle still there?

why not try bypassing minidisk and play the sequencer audio directly into the computer?