In Darkside (the soundtrack from Silent Threat), if the allied arrival cue "plays" during the battle music, the music stops for the rest of the mission. This happens because the entry for this cue is "none.wav," and this causes the music to stop if it is called. A fixed version of this soundtrack is provided below. (The 11th line is the one that was changed.)
;;FSO 3.6.0;; #SoundTrack Start
;;FSO 3.6.0;; $Soundtrack Name: FS1-10: Darkside
;;FSO 3.6.9;; +Cycle: FS1
;;FSO 3.6.8;; +Allied Arrival Overlay: NO
;;FSO 3.6.0;; $Name: m10_NRML1.wav 39.8 52920 ; Normal 1
;;FSO 3.6.0;; $Name: m10_AARV1.wav 3.8 44100 ; Allied Arrival during Normal
;;FSO 3.6.0;; $Name: m10_EARV1.wav 1.8 44100 ; Enemy Arrival during Normal
;;FSO 3.6.0;; $Name: m10_BTTL1.wav 15.8 66150 ; Battle 1
;;FSO 3.6.0;; $Name: m10_BTTL2.wav 11.8 66150 ; Battle 2
;;FSO 3.6.0;; $Name: m10_BTTL3.wav 9.8 66150 ; Battle 3
;;FSO 3.6.0;; $Name: m10_AARV1.wav 3.8 44100 ; Allied Arrival during Battle
;;FSO 3.6.0;; $Name: m10_EARV2.wav 3.8 44100 ; Enemy Arrival during Battle
;;FSO 3.6.0;; $Name: m2_VICT1.wav 1.8 52920 ; Victory 1 ( goal completed )
;;FSO 3.6.0;; $Name: m2_VICT2.wav 26.8 52920 ; Victory 2 ( all enemies dead, goals completed )
;;FSO 3.6.0;; $Name: none.wav 1.8 36150 ; Goal Failed
;;FSO 3.6.0;; $Name: m1_DEAD.wav 19.8 35800 ; Player dies
;;FSO 3.6.0;; $Name: none.wav 00.0 00000 ; Normal 2
;;FSO 3.6.0;; $Name: none.wav 00.0 00000 ; Normal 3
;;FSO 3.6.0;; #SoundTrack End
In case you're wondering, this problem was also in the original Silent Threat.