I would say that your problem is not the species_defs.tbl but sounds.tbl. Seems like you are missing the flyby sounds from the end of the sounds.tbl. Every species must have these defined.
Normally there are following entries:
#Flyby Sounds Start
$Terran: 0 T_flyby1.wav, 0, 0.75, 1, 200, 400 ; * Terran ship1 flyby player sound (3d sound)
$Terran: 1 T_flyby2.wav, 0, 0.75, 1, 200, 400 ; * Terran ship1 flyby player sound (3d sound)
$Vasudan: 0 V_flyby1.wav, 0, 0.85, 1, 200, 400 ; * Vasudan ship1 flyby player sound (3d sound)
$Vasudan: 1 V_flyby2.wav, 0, 0.85, 1, 200, 400 ; * Vasudan ship1 flyby player sound (3d sound)
$Shivan: 0 S_flyby1.wav, 0, 0.75, 1, 200, 400 ; * SHIVAN ship1 flyby player sound (3d sound)
$Shivan: 1 S_flyby2.wav, 0, 0.75, 1, 200, 400 ; * SHIVAN ship1 flyby player sound (3d sound)
#Flyby Sounds End
If you added a new species, make sure you have entries for that particular species. And also correct changes in asteroids.tbl and icons.tbl. If you like you can PM the table to me and i can take a look at it.