We do have a few reports of “choppy” or “stuttering” playback in 2.0.4 on OS X , but the problem is not reproducible on any of our machines.
So I hope you won’t mind a few questions.
What application produced the problem files? Are you using Soundflower?
If you import audio into Audacity that sounds OK in other players, then export it from Audacity as 16-bit WAV at 44100 Hz project rate (see bottom left of the Audacity window), and then play it in iTunes, does it still sound OK?
Do you drag the audio rightwards after importing it into Audacity, so that there is white space in the track before the audio waveform starts?
Do you have multiple files in one project window?
If you Tracks > Mix and Render the imported audio in Audacity, does that stop the crackle?
Exactly what device are you using for playback? What are your settings for that device in /Applications/Utilities/Audio MIDI Setup? What Audacity project rate do you usually use?
Do you have Transport > Overdub (on/off) switched on (checked)? If so, does turning Overdub off help?
Can you provide a link to an example file that crackles when you play it in Audacity? For example, you could upload it to dropbox, sendspace.com or similar.
Gale