There are several ways of avoiding the need to use -s on the command line:

P:\test>assoc .pl
.pl=Perl

P:\test>ftype Perl
Perl="c:\perl\bin\perl.exe" -sw "%1" %*

P:\test>type test.pl
#! perl -slw
use strict;

print 'hello' if our $hello;
print 'world' if our $world;

P:\test>test -hello -world
hello
world

P:\test>ftype Perl="c:\perl\bin\perl.exe" -w "%1" %*
Perl="c:\perl\bin\perl.exe" -w "%1" %*

P:\test>set PERL5OPTS=-s

P:\test>test -hello -world
hello
world
[download]

Whether either method would work for the op's problem I have no idea as I've never used perl2exe. Of the two, I would think that setting PERL5OPTS=-s is the more likely to work if either do.