Try with -nosound
enabled. Your mention of pilot chatter affecting things might suggest it being an audio issue, so disabling sounds is a pretty surefire way to isolate the problem on sound system - if problem disappears, correlation is quite clear; if not, we'll have to look elsewhere.
You could also check that you have the in-game text-to-speech disabled on missions; if the TTS conflicts with existing messages or if TTS is not working correctly, it could cause problems (this is mainly a shot in the dark though).
What sort of sound card are you using? What setting do you have on your FSO Launcher's Audio/Joystick panel? Generic Software is the default that should be tried (other options may be available, and they might work perfectly well, but if you have something else selected and it causes problems, choose Generic Software and retry.
Also, check that you don't have any processes running amok and grabbing CPU processing power from the game exec; the problems you described are consistent of something interrupting the game's process momentarily (it could be related to sound driver crapping itself out, or any other process with equal priority to FS2_Open that hogs the CPU.
Also mentioning what operating system you use would be helpful (default assumption that I tend to use is WinXP, but it can sometimes be wrong).
And you'll get used to quick replies on these forums I think.