Since you're not filtering the directory read, you may be getting more than just files in your @FILES array. Also, you can use the module File::Copy to actually do the file moving for you. Given this, consider the following (untested):

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

my $newDir = '/home/iphone/Maildir/new';
my $curDir = '/home/iphone/MailDir/cur';

opendir my $dir, $newDir or die $!;
my @FILES = grep { !/^\./ and -f "$newDir/$_" } readdir($dir);
closedir $dir;

move( "$newDir/$_", "$curDir/$_" ) for @FILES;
[download]

Of course, try it on a scratch directory with sample files before using it on your emails.

Hope this helps!