Hi Rob,
possible reason you hear the sounds overlapping and playing at the same time is because your blockly expression is put into a repeat loop. Try removing the blocks from your "repeat 1 times" block.
When I tried your scene, the sound effects played at the right time (Tie engine sound when the tie fighter lifts off and flies away, darth vader music when the other spaceship enters the hangar).
On slower computers, the "pause for X sec." may take longer than for other machines. This could be another reason for sound effects not playing on time. I'd recommend you to play sound effects right after a "move" block has happened to make sure that the sound effect is motion dependent, not time dependent.
To help you get a better overview of your blockly code you can put bigger block-chunks into functions and call them like shown below. This helps you in creating more manageable code.
(Click for full size)

Let me know if the problem with playing back the sound persists after removing the loop.
Cheers,
Stefan