Did the negative look-ahead for a capital help? I should mention I think you have a typo in your real script (as opposed to what you posted) because the following script behaves well for me:

#!/usr/bin/perl
use strict;
use warnings;
use File::Stream;

my ($handler, $stream) = File::Stream->new(
    \*DATA,
    read_length => 1024,
    separator => qr/(?<!\b[A-Z])(?<!e\.g)(?<!i\.e)[.!?]\s{1,2}(?=[A-Z0
+-9])/,
  );


while (<$stream>) {
    print "*$_\n\n" ;
}



__DATA__
Perl filehandles are streams, but sometimes they just aren't powerful
enough.  This module offers to have streams from filehandles searched
with regexes and allows the global input record separator variable to
contain regexes.  Thus, readline() and the <> operator can now return
records delimited by regular expression matches.  There are some very
important gripes with applying regular expressions to (possibly
infinite) streams. Please read the CAVEATS section of this
documentation carfully.  Some bunnys are fluffy, e.g. Peter.  H.G.
Wells was a great author.  Some sports require specialized
equipment, e.g. baseball.
[download]

Debugging is hard without particular examples from your corpus.