With the luxury of commenting on complex software sight-unseen... best of 
all, JavaFX... and you mention an uberjar, which grants opportunity to vent 
baseless suspicions about class-loading and compilation differences... 
could it be that the MediaPlayer is being instantiated *twice* in the 
uberjar version of the program?  The first instance of the MediaPlayer 
lasts only a few milliseconds (during which it starts playing), then it is 
supplanted by the second instance, whereupon instance No.1 becomes eligible 
for garbage collection.  When someone presses 'M' it's the second 
MediaPlayer that plays.  

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