Yep, did all that. I tried many different ways to get the sounds to play but to make it a bit clearer I used this most basic method (among many others) to eliminate any change I'd forgotten to transfer something, made a scripting error etc.......
Desert Island scenario:
Basic Mission - one (player) unit, one Game Logic with one waypoint. Waypoint set to true and set to play one of my sound effects.
Description file, in the mission folder defines the sounds in the sounds folder of the mission.
Sounds folder (inside the mission folder) with the sounds I am trying to use inside.
Result: sounds play
Everon Scenario.
Copied and pasted the unit, game logic and waypoint to Everon map. Copied and pasted Description file to Everon mission folder. Copied and pasted Sound folder (with contents) to mission folder.
Thus both missions (contents and all) are identical other than being on different islands, no errors possible.
Result: my sound doesn't play (default game sounds do as normal)
Reverse the above, taking everything from Everon back to another new, empty Desert Island scenario. Result - sounds play.
Repeat all the above for Kolgujev and Malden. Same results - no sound, but when the same are returned to a new desert island map it all works again.
Nothing has been edited in any way (ie no names etc) - they are exactly as they appear by default when they are created, with the single exception that the Game logic waypoint is set to play a sound. Thus there are no references specific to Desert Island in the setup, so changing location should have no effect. The sounds are long enough that any difference in loading time will not allow them to be missed. And to be sure, I did the whole thing again with a trigger activated sound in addition, with the same result.