Honestly, I find it very hard to read your code (and so, hard to debug) because it's not structured well. Consider refactoring it a bit, so you have something like this:

# Top level
my $choice = get_choice();
do_ip_manual() if $choice == 1;
do_ip_fromfile() if $choice == 2;

# Lower level
sub do_ip_manual {
    my ($user, $pass) = get_auth();
    ...
}

# Even lower level
...
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... instead of lots of long if/else blocks.

It'd be easier to debug failures if you checked the return values of all those external executions. You're assuming they succeed.

my $ret = system "`xcopy "C:\\Program Files\\UltraVNC\\*.*" "\\\\$ip\\
+C\$\\Program Files\\UltraVNC\\*.*" /r/i/c/h/k/e/Y";
die "xcopy failed" if $ret;
$ret = 0;
...
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If you'd like to improve your code generally, here are a few tips (good on you for using strict and warnings, you've just saved yourself a handful of head hair):

open(DAT,">>$resultOutput") || die("Cannot Open File");
print DAT "Bad username or password on the following machines:\n";
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Be careful using || when performing error checking. It's a better idea to use or. You'll get bitten by precedence if you do this:

open DAT, ">>$filename" || die "foo";
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Because || has higher precedence than the function call or the comma operator, that won't die if the open fails. It's evaluated like this:

open DAT, (">>$filename" || die "foo");
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... and ">>$filename" is never logically false.

Also: it's good to get into the habit of using lexical filehandles:

open(my $dat, ">>", $resultOutput")    or die("Cannot Open File");
print $dat "Bad username or password on the following machines:\n";
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... for reasons described on this Perl5Wiki page.