I would try reseating all the ribbon cables on the driver board and CPU. This 'cleans' the pins and has cured several bizarre sound issues for me in the past.
James
I turned the machine on last night and the sound problem was present from the outset, I did not even have to start a game. I went through the Switch Test to see if a switch was stuck on but couldn't find any problematic switches. I then opened up the backbox and reseated the connector on the WPC Audio Board, and the sound problem disappeared. I had done this previously and it didn't fix the problem, so I ignored this as a solution up until now. Hopefully if the problem re-occurs, the fix will be as simple as reseating the connector on the Audio board.
Interestingly, the "whoosh" sound that I described in my original post was a combination of the "Buy-In after Game Over" sample and the "Match Feature" sample - both of these sounds are missing from the Sound + Music menu.
Matthew