Yeah, that's definately what's going on here. The li_cruiser guns are definately two-barrelled. Go to the Effects.ini, find the effect listed for the Flash (this is the easiest method) and then assign a snd_effect = "whatever the name of the sound you want to hear played" to that Effect.
BTW, I not only did this, for the XML Toolkit Mod, 1.2, but I also re-mixed the capgun fire noise so that it's quieter- this is necessary, because otherwise the doubled sound (FL treats two identical sounds playing at the exact same time as one sound, doubled in volume) results in distortion and annoying audio crackling, along with noticable lag (caused by FL's sound-handling code desperately trying to mix the sound channels down to a non-cutoff level, I suspect). So fixing this both made things sound appropriate and reduced the lag of multi-fire weapons.
So, uh... look at how this was solved in the Toolkit, if you're stuck. Basically, you just have to follow the INI references... like everything else