Hi deadpickle,

The reason you're getting 1 2 again, instead of 5 6, can be quickly visualized with the following 2 modifications:

First, add Data::Dumper to the top of the program:

use strict;
use warnings;
use Data::Dumper;        # Add this line
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And then display what's happening in the subroutine compile by adding a printf near the end:

sub compile{
    $all = $waybox->index('end');
    print "$all\n";
    for(my $num = 1;$num <= $all;$num++){
        my $new = $num-1;
        my $sel = $waybox->get($new);
        print "TFD> sel <$sel>\n";
        chomp ($sel);
        push(@latlong, $sel);
    }
    # liverpole -- Add a "Temporary for debug" print statement
    printf "TFD> latlong => %s\n", Dumper(\@latlong);
    $go = 1;
}
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What you'll then see, following your instructions above, is that when you connect the first time (with points "1 2" and "3 4"), you get the expected:

TFD> latlong => $VAR1 = [
          '1 2',
          '3 4'
        ];
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But the second time you connect, after adding "5 6", you get:

TFD> latlong => $VAR1 = [
          '1 2',
          '3 4',
          '1 2',
          '3 4',
          '5 6'
        ];
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So you probably just need to clear the points from the @latlong, perhaps at the end of the block in sub sftp:

    if ( $go == 1 ){
        # ...
        @latlong = ( );
    }
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Note, however, that you may need to lock the shared data structure @latlong, both in the parent thread and the child, wherever it is being changed (unless your flag $go is correctly handling any race conditions).

Update:  Looking at some of your code more in-depth, you may want to put a delay everywhere you have a tight loop, so that it doesn't hog cpu time.  For example:

    for(;;){
        if( $progress == 0){last}
        # Pause for 1/10th of a second to be a good citizen
        select(undef, undef, undef, 0.1)
    }
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