using the perl debugger I found a little bit about the problem. The output I received seems to be possibly from the thread:

Attempt to free unreferenced scalar: SV 0x43314ac, Perl interpreter: 0x41083fc a t GRRUVI-v0.45.pl line 133. at GRRUVI-v0.45.pl line 133
Attempt to free unreferenced scalar: SV 0x5f53f6c, Perl interpreter: 0x4c9c85c a t GRRUVI-v0.45.pl line 134.
at GRRUVI-v0.45.pl line 134 GLib-GObject-CRITICAL **: g_object_steal_qdata: assertion `G_IS_OBJECT (object)' failed during global destruction. at GRRUVI-v0.45.pl line 0 eval {...} called at GRRUVI-v0.45.pl line 0
GLib-GObject-CRITICAL **: g_object_unref: assertion `G_IS_OBJECT (object)' faile d during global destruction. at GRRUVI-v0.45.pl line 0

and refers to the code lines:

#################################################
#Threads
my $thread_gps = threads->new( \&gps);
my $thread_sftp = threads->new( \&sftp);

#################################################
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though the output is a little strange with it referring to line zero of the program. The threads are stopped by the join command. I wonder if the threads I have are being exited incorrectly? I'm not sure what this attempt to free unreferenced scalar is?!

####################Threads####################
#-------------------GPS-------------------
sub gps {
    my $gps_device;
    while (1) {
        goto END if $die == 1;
        if ($gps_start == 1) {
            $gps_device = GPS::NMEA->new(Port => $gps, Baud => 4800);
            
            for (;;) {
                #stops the warnings in the GPS device module
                local $^W = 0;
                
                ($ns,$lat,$ew,$lon) = $gps_device->get_position;
                
                goto END if $die == 1;
                last if $gps_start == 0;
                sleep 3;
            }
            undef $gps_device;
        } else {sleep 4}
    }
    END:
}

#-------------------SFTP-------------------
sub sftp{
    $|++;
    while(1){
    
        if ( $die == 1 ){ goto END };
        if ( $sftp_start == 1 ) {
            my $seconds = 120;
            my %args = (host=>$server, user=>$username, timeout=>$seco
+nds);
            my $sftp = Net::SFTP::Foreign->new(%args);
            #$error = 1 if $sftp->error;
            
            for (;;) {
                if (defined $ns){
                    #The GPS file Functions
                    my $gps_loc = $sftp->open( "$gps_remote/$gps_file"
+ , SSH2_FXF_CREAT|SSH2_FXF_WRITE) or $sftp->error;
                    my $new_lat;
                    my $new_lon;
                        
                    #adjust the gps position into decimal
                    if ($ns eq 'S'){
                        $new_lat = "-$lat";
                    }
                    else {
                        $new_lat = $lat;
                    }
                    if ($ew eq 'W'){
                        $new_lon = "-$lon";
                    }
                    else {
                        $new_lon = $lon;
                    }
                    $sftp->write( $gps_loc, "$nick $new_lat $new_lon")
+;
                    $sftp->close( $gps_loc);
                }
                    
                #VC Base
                if ($job == 2) {
                    #Upload the uasposition file
                    $sftp->put( $uasposition_local, $uasposition_remot
+e);
                    #update the counter
                    $count_uasposition = $count_uasposition + 0.05;
            
                    #Create the attribute file
                    my $stat_final = Net::SFTP::Foreign::Attributes->n
+ew;  
                    #open the files on the server; flagged for writing
+ and creating
                    my $waytemp = $sftp->open( $waytemp_remote) or $sf
+tp->error;
                    my $wayfinal = $sftp->open( $wayfinal_remote, SSH2
+_FXF_CREAT, $stat_final) or $sftp->error;
                    #Read the stats of the files and check which is ne
+wer
                    my $stat_temp = $sftp->fstat($waytemp);
                    $stat_final = $sftp->fstat($wayfinal);
                
                    #check to see if temp is newer than final
                    if (( $stat_final->mtime) < ($stat_temp->mtime)) {
                        #Turn verification window on
                        $verify = 1 if $verify == 0;
                        if ( $verify == 2) {
                            #read the lines in then write to the wayfi
+nal file if it is newer then the waytemp file
                            my $print = $sftp->readline( $waytemp);
                            my $wayfinal = $sftp->open( $wayfinal_remo
+te, SSH2_FXF_TRUNC|SSH2_FXF_WRITE) or $sftp->error;
                            #write to the file and add to the counter 
+if it does write
                            $sftp->write( $wayfinal, $print);
                            $count_waypoint = $count_waypoint + 0.05;
                            $verify = 0;
                        }
                        if ( $verify == 3) {
                            #get time and print it to the final file
                            my $time = time;
                            $stat_final->set_amtime( $time, $time);
                            $sftp->fsetstat( $wayfinal, $stat_final);
                            $count_waypoint = $count_waypoint + 0.05;
                            $verify = 0;
                        }
                        #close the files on the server
                        $sftp->close( $waytemp);
                        $sftp->close( $wayfinal);
                    }
                }
                
                #Met Base
                if ($job == 3){
                    #Open the waytemp file on the server; for write on
+ly
                    if ( $verify == 4) {
                        my $waytemp = $sftp->open( $waytemp_remote, SS
+H2_FXF_TRUNC|SSH2_FXF_WRITE) or $sftp->error;
                        #Write the waypoints to the waytemp file
                        $sftp->write( $waytemp, $coords);
                        $sftp->close( $waytemp);
                        $count_waypoint = $count_waypoint + 0.05;
                        $verify = 0;
                    }
                }        
                sleep 1;
            }
            if($sftp_start == 0){ last};
            if($die == 1){ goto END };
            #undef $sftp;
        }else { sleep 1 }
    }
    END:
}

#################################################
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