It seems to me that there is no reason to use system to call your perl script. Just set local values for @ARGV and call do:

# instead of system perl...
{
  local @ARGV = ("G:/PUB_HLTH/blah/blah", "G:/PUB_HLTH/blah/blah2");
  do '20_October_2004_K.pl';
}
[download]

I do not know whether this will fix your problem, but it might. You don't seem to close the file, and if you have a series of several different processes that open and append to the file without closing it, they may be stepping on each others' toes (although as each process exits, it should implicitly close the file).