This only happens with Internet radio:

When the radio loses its connection (as alas still often happens) the digital lock on the Squeezebox 
output is lost. My system responds to that by outputting an unpleasant crackling sound. The same 
happens when stations are stopped or paused.

The lock is maintained when pausing/stopping music files that are played from disk, no problems 
there. In this case the offender is my Behringer digital equalizer.