If your program is the only one writing to these dirs, you can sort them by mtime, as you can for files that appear in /main:

my @dirs = ('/dir1/', '/dir2/', '/dir3/', '/dir4/', '/dir5/', '/dir6/'
+,);

my @newfiles = sort {-M $b <=> -M $a} grep {-f } glob("/main/*");
my @seq = (sort {-M $b <=> -M $a} @dirs) x int( 1 + @newfiles/@dirs);

for (@newfiles) {
    my $status = system '/bin/cp', '-f', $_, shift @seq;
    die 'Copy failed for ', $_, ': Child Error ', $?, $! if $status;
    unlink $_ unless $status;
}
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If mtime of the inodes is not helpful, you'll need to keep some sort of persistent data file. I also would like to know why each of the other solutions failed.

After Compline,
Zaxo