I've created new disks before in bulk.  Are you adding or creating disks?  Got more of your code to show?

I did not want to do a code dump, but here you go

1. package VManagement;
2. # Paul Givens
3. # Evaluator Group
4. # 6/11/2013
5. # A package for manipulaing virtual machines through vSphere
6. # Public functions
7. # addDisks
9. use strict;
10. use warnings;
12. # I do not know why this lib is needed, delete it for a fun time
13. use lib "/usr/lib/vmware-vcli/apps";
15. use Exporter;
16. use VMware::VIRuntime;
17. use AppUtil::VMUtil;
19. # Making a module
20. our @ISA       = qw( Exporter );
21. our @EXPORT_OK = qw( addDisks );
22. our @EXPORT    = qw( addDisks );
24. # Declarations
25. sub addDisks;
26. sub atomicAddDisks;
28. # addDisks
29. # a function to add disks to a virtual machine
31. sub addDisks{
32.   # Getting arguments
33.   (my $viServer, my $login, my $password, my $verbose) = @_;
35.   # Setting the global variables
36.   $ENV{VI_SERVER}   ="$viServer";
37.   $ENV{VI_USERNAME} ="$login";
38.   $ENV{VI_PASSWORD} ="$password";
40.   # Connecting
41.   Opts::parse();
42.   Opts::validate();
43.   Util::connect();
45.   # TEST start
46.   my @diskSizes = (1,2,1);
47.   my @datastores = ("zebi1n", "zebi1n", "zebi1n");
48.   # TEST stop
50.   if ($verbose) {print "Connected to server\n";}
51.   atomicAddDisks("paul-vm1", \@diskSizes, \@datastores, $verbose); 
52.   # Disconnecting
53.   Util::disconnect();
54. }
56. sub atomicAddDisks{
57.   # Getting arguments
58.   (my $vmName, my $diskSizesRef, my $datastoresRef, my $verbose) = @_;
60.   # Dereferencing
61.   my @diskSizes  = @$diskSizesRef;
62.   my @datastores = @$datastoresRef;
63.   # Kb to Gb conversion factor
64.   my $scsiNum  = 0;
65.   my @devSpecs = ();
66.   my $vmView   = Vim::find_entity_view(view_type => 'VirtualMachine',
67.          filter => { 'name' => $vmName } );
69.   my $vmDevices = $vmView->config->hardware->device;
70.   my $diskFilename;
71.   my $diskFilenameIncrement = 0;
72.   my $diskFilenameCur;
73.   my $diskNum = 0;
75.   foreach my $vmDevice (@$vmDevices) {
76.          # Adjusting the diskNum for disks already present 
77.          if (ref($vmDevice) eq 'VirtualDisk') {
78.                 $diskNum++;
79.                 }
80.   }
81.   # Search virtual SCSI controller
82.   my $controller;
83.   my $numController = 0;
84.   foreach my $vmDevice (@$vmDevices) {
85.          if (ref($vmDevice) =~/VirtualBusLogicController|VirtualLsiLogicController|VirtualLsiLogicSASController|ParaVirtualSCSIController/) {
86.                 Util::trace(1, "SCSI controller found : $&\n");
87.                 $numController++;
88.                 $controller = $vmDevice;
89.          }
90.   }
91.   my $controllerKey = $controller->key;
92.   # Set new unit number (7 cannot be used, and limit is 15)
93.   my $unitNum;
94.   my $vdiskNumber = $#{$controller->device} + 1;
95.   if ($vdiskNumber < 7) {
96.          $unitNum = $vdiskNumber;
97.   }
98.   elsif ($vdiskNumber == 15) {
99.          die "ERR: one SCSI controller cannot have more than 15 virtual disks\n";
100.   }
101.   else {
102.          $unitNum = $vdiskNumber + 1;
103.   }
105.   for(my $i = 0; $i < @datastores; $i++) {
106.          # Conversion to GB
107.          my $disksize =  $diskSizes[$i] * 1048576;
108.          my $datastore = $datastores[$i];
109.          # Increase the disk number to represent the machine to be added
110.          $diskNum++;
111.         
114.          $diskFilename = "[$datastore] paul-vm1/paul-vm1_" . "$scsiNum" . "_" . $unitNum . ".vmdk";
116.          # Build virtual spec data object
117.          my $diskMode = VMUtils::get_diskmode(
118.                 nopersist   => "",
119.                 independent => ""
120.          );
122.          if ($verbose){
123.                 print "SPECS\n";
124.                 print "\tVM Name:\t$vmName\n";
125.                 print "\tDisk Name:\t$diskFilename\n";
126.                 print "\tController Key:\t$controllerKey\n";
127.                 print "\tUnit Number\t$unitNum\n";
128.                 print "\tDisk Size\t$disksize\n";
129.          }
131.          my $devSpec = VMUtils::get_vdisk_spec(
132.                 vm            => $vmView,
133.                 backingtype   => 'regular',
134.                 diskMode      => $diskMode,
135.                 fileName      => $diskFilename,
136.                 controllerKey => $controllerKey,
137.                 unitNumber    => $unitNum,
138.                 size          => $disksize);
140.          ###########################################
141.          # Run ReconfigVM method (in VMUtils package)
142.          # with previously defined specs
143.          ###########################################
145.          push(@devSpecs, $devSpec);
146.          #increase the unit number for each device
147.          $unitNum++;
148.   }
149.   my $vmSpec = VirtualMachineConfigSpec->new(deviceChange => \@devSpecs);
150.   $vmView->ReconfigVM(spec => $vmSpec);
152.   #my $vmSpec = VirtualMachineConfigSpec->new(deviceChange => [$devSpecs[0]]);
153.   #$vmView->ReconfigVM(spec => $vmSpec);
154.   #my $vmSpec = VirtualMachineConfigSpec->new(deviceChange => [$devSpecs[1]]);
155.   #$vmView->ReconfigVM(spec => $vmSpec);
156.   #my $vmSpec = VirtualMachineConfigSpec->new(deviceChange => [$devSpecs[2]]);
157.   #$vmView->ReconfigVM(spec => $vmSpec);
159. }

Since you're adding an existing VMDK, any chance you're adding it twice or it's already attached to that VM? 

I dont think so, If that was true, why could I add the three individual machines by array index as apposed to passing it the array of three items

Do this, add "print Dumper($vmSpec)" before line 150.  We can eyeball the spec sent to the API.

"key => -1" works fine for me:

Since I am adding a bunch of pre-existing disks, what I do is this:

- locate the disks based on the datastore and folder location using datastore browser (SearchDatastoreSubFolders call).

- do an inventory of the controllers so that I can reference the controller keys when needed

- do an inventory of the virtual disks currently attached to the vm (so that I know if adding more disk to a particular virtual node makes sense).

then loop through the diks that you have found from the datastore and are supposedly attaching disks to.

                    my $backing = @$disks[$i]->diskType->new (

                                diskMode => 'independent_persistent',

                                fileName => $result->folderPath . @$disks[$i]->path,

                                );

                        my $connectInfo = VirtualDeviceConnectInfo->new (

                                allowGuestControl => 0,

                                connected => 1,

                                startConnected => 1,

                                );

                        my $devInfo = VirtualDisk->new (

                                backing => $backing,

                                controllerKey => $ctrlKey,

                                unitNumber => $unit,

                                connectable => $connectInfo,

                                key => -1,

                                capacityInKB => @$disks[$i]->capacityKb,

                                );

                        $devspec[$i] = VirtualDeviceConfigSpec->new(

                                operation => VirtualDeviceConfigSpecOperation->new('add'),

                                device => $devInfo,

                                );

Once finish the loop, construct the $spec and run reconfigVM (or reconfigVM_task):

          my $spec = VirtualMachineConfigSpec->new(deviceChange => [@devspec] );    

                if (@devspec) {

                        print "Reconfig VM with disk changes...\n";

                        # Asynchronous vs Synchronous execution

                        #eval { $vm->ReconfigVM(spec => $spec); };

                        eval { $vm->ReconfigVM_Task(spec => $spec); };

                        if ($@) { print "Reconfiguration failed.\n $@";}

                        else {print "Disks added successfully.\n"; }

                } else { print "Nothing to add!\n"};