one ship shooting 6 missiles at a time at one target shouldnt be causing that much of a problem, especially not when those are the only ships that are visible at the time...
Yeah you wouldn't think so. I have had a ship shotting 12 phase missles, from only 1 weapon type set mind you, and I don't experience any problems. I'm really at a loss as to what your problem may be. Maybee there is something wrong with the MissileTravelEffect data within the weapon, but you would think that the Dev.exe would pick it up, and that dosn't explain why its only happen to some of them some of the time.
If I was a betting man, I would say it was something simple like a conflict with the weapon count or something like that, but really its quite impossible to know without having looked through the file's and comparing them.
Anyhow I wish you luck with figuring it out.