> It's not impossible that PulseAudio tries to play higher quality audio or simply uses the device differently.
Pulseaudio mixes sound from several applications, unlike Alsa. Alsa just configures your soundcard for that one stream, Pulseaudio has no such luxury.
In order to mix relatively small buffers (because latency), it needs to do timing. If your soundcard has problem with timing (and many do!), you will get crackling. The good news is, that the problem with timing can be only at specific frequencies; in the past, I had a computer with Nvidia Ion and it did this with 44,1kHz audio. With 48kHz, everything was OK. So fixing the output at 48kHz by forcing Pulse to mix at this frequency fixed the crackling.