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.

#11929 First ask yourself `How would I do this without a computer?' Then have the computer do it the same way.

In reply to Re^3: End of sentence regex excluding " i.e." and " e.g." by kennethk
in thread End of sentence regex excluding " i.e." and " e.g." by jabowery

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.