Did more work on this by installing latest Soundblaster drivers and control panel, which made the 'thumping' effect worse. Checked back on previous driver / control panel combinations, all of which introduced various different oddities. At that point, decided to switch to optical output, which gave a much smoother sound with - for all practical purposes - an absence of thumping. They can still be heard at very low level, together with occasional drum fills, by splitting the tracks, but not at any sort of level to cause a problem.

Spectrum analyser shows these thumps to be between about 50 and 100Hz and, although soundcard was set to front L&R output only, I wonder if it was allowing some of the subwoofer feed - which would be around that frequency - to 'bleed' through.

It also made me wonder - given that these sounds are exactly in time with the music - if they are used as some sort of low-frequency metronome, which would be far less obtrusive than conventional 'click' track that leaks quite readily from performer's headphones.