Great mod Sailor Steve.
I tried replacing several files and am now pretty certain it's
Submarine_Surface_INT.wav
Replace it with the default file and the thumping has gone away. You can also try deleting it altogether (or rename it to Submarine_Surface_INT.wav.bak)
I think it always happened when I used Persicope-Depth and Surface-The-Boat commands during time compression. Practically every time.
Remark: Initially I also had Submarine_GQ_battle_stations_INT.wav disabled (as suggested by limkol) so half my testing time were without that one too. Disable it as well, to be sure, and see if the thumping goes away.
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