http://www.pinwiki.com/wiki/index.php?title=Sega/Stern_White_Star_Repair#CPU_.2F_Sound_Board
Interesting item from the Pinwiki about using a newer revision of the cpu in #starshiptroopers "If the CPU/Sound board II is used in early games, Starship Troopers for instance, some sounds may not render correctly."
http://www.pinwiki.com/wiki/index.php?title=Sega/Stern_White_Star_Repair#Sound_problems
Maybe try probing U6 while the game is working correctly, then comparing that to when it's malfunctioning? See if your logic probe shows the sound CPU is hanging or if the problem is in the BSMT or the DAC?