Whenever I use the phasers, the little point lights and sprites that are usually positioned where the beam starts on the hull instead flash all around the ships at random places.
it happens....
I got that problem with CG's galaxy back in the day... I guess you can track down the problem to the size of the firing arc.
if it's too big, and the actual beam fires too fast, the effect tends to lag up or not refresh correctly.
that, and it can also be a matter of graphic load, and texture processing speed.
try using the KM sovereign with blind firing and do a random sweep in a map such as Beol 4 or Vesuvi dust cloud, and repeat the process in an empty map such as Void or Riha.
if you still got the bug, it's a matter of graphics... if not, it's a matter of hardpoints.