Inelegant in the extreme, but I dug out some old Windows-only code that I used years ago on an ancient Perl that still seems to work with latest Strawberry Perl.

use strict;
use warnings;

sub read_file_contents
{
   my $fname = shift;
   open( my $fh, '<', $fname ) or die "error: open '$fname': $!\n";
   local $/ = undef;    # slurp mode
   my $s = <$fh>;
   close($fh);
   return $s;
}

# Run a Windows executable synchronously.
# Return a three element list:
# the return code; the stdout of the command; and the stderr of the co
+mmand.
# Die if something goes wrong.
sub run_cmd_sync
{
   my ( $exe, $cmd, $workdir ) = @_;
   defined($workdir) or $workdir = ".";

   require Win32::Process;

   my $tmpout = "klink-out-$$.tmp";
   my $tmperr = "klink-err-$$.tmp";

   -f $exe or die "error: file '$exe' not found";

   local *SAVOUT;
   local *SAVERR;

   # save original stdout and stderr
   open( SAVOUT, ">&STDOUT" ) or die "error: open SAVOUT: $!";
   open( SAVERR, ">&STDERR" ) or die "error: open SAVERR: $!";

   open( STDOUT, '>', $tmpout ) or die "error: can't redirect stdout";
   open( STDERR, '>', $tmperr ) or die "error: can't redirect stderr";

   Win32::Process::Create(
      my $hProc,    # process object
      $exe,         # executable
      $cmd,         # command line
      1,            # inherit handles
      Win32::Process::NORMAL_PRIORITY_CLASS(),
      $workdir      # working dir
   ) or die "error: Win32::Process::Create: $^E ($!)";
   my $pid = $hProc->GetProcessID();

   # parent continues (redirect back to original) ...
   close(STDOUT);
   close(STDERR);
   open( STDOUT, ">&SAVOUT" ) or die "error: open SAVOUT: $!";
   open( STDERR, ">&SAVERR" ) or die "error: open SAVERR: $!";

   print "started exe:$exe (cmd:$cmd) ok, pid=$pid.\n";

   my $rc = 0;
   $hProc->Wait( Win32::Process::INFINITE() ) or die "error: Wait: $^E
+ ($!)";
   $hProc->GetExitCode($rc) or die "error: GetExitCode: $^E ($!)";

   my $outstr = read_file_contents($tmpout);
   my $errstr = read_file_contents($tmperr);
   unlink($tmpout) or die "error: unlink '$tmpout': $!\n";
   unlink($tmperr) or die "error: unlink '$tmperr': $!\n";

   return ( $rc, $outstr, $errstr );
}

my ( $rc, $outstr, $errstr ) = run_cmd_sync(
   $^X,
   'perl -e "print q{hello stdout}; print STDERR q{hello stderr}"',
   '.'
);
print "rc='$rc'\n";
print "stdout='$outstr'\n";
print "stderr='$errstr'\n";
[download]

started exe:C:\Strawberry\perl\bin\perl.exe (cmd:perl -e "print q{hell
+o stdout}; print STDERR q{hello stderr}") ok, pid=3132.
rc='0'
stdout='hello stdout'
stderr='hello stderr'
[download]

In case it's of use, running this simpler and more portable test program tt1.pl works from the Windows shell at least, but will probably hit the same problems you are currently suffering if run without a shell.

# Test program tt1.pl

use strict;
use warnings;

# Run a command without invoking the command shell.
#   exe is the command name
#   @_ contains the command line arguments (including argv[0])
sub run_cmd_noshell
{
   my $exe = shift;
   print "run '$exe' with args:\n    '@_'\n";
   system { $exe } @_;
   my $rc = $? >> 8;
   $rc == 0 or warn "error: exit code=$rc\n";
}

run_cmd_noshell($^X, $^X, '-le', 'print q{hello one};');
run_cmd_noshell($^X, 'perl', '-le', 'print q{hello two}; exit 42;');
[download]

run 'C:\Strawberry\perl\bin\perl.exe' with args:
    'C:\Strawberry\perl\bin\perl.exe -le print q{hello one};'
hello one
run 'C:\Strawberry\perl\bin\perl.exe' with args:
    'perl -le print q{hello two}; exit 42;'
hello two
error: exit code=42
[download]