To echo what tilly said, don't use 'flag' for a variable name unless you're talking about a square or rectangle of cloth. Why not something more interesting like $seenJunkYet instead?

I'd rather go for something like

#  Skip header junk
while(<>) {
  last if /end of header junk/;
}
#  Start processing real data
while(<>) {
  #  But quit if we see junk starting up again
  last if /start of trailer junk/;

  # Do useful stuff here
}
[download]

That way there aren't any flag variables. It's more lines of code, but it reads more easily.