I don't understand why your code displays the strange results it does. Here are some observations.

If I change the last loop to read:

    while(1){
        shmread($key,$message,0,99);
        ++$t;
        my $t_copy       = $t;
        my $message_copy = $message;
        print "$t_copy - $message_copy is ", $t_copy - $message_copy, 
+"\n";
        sleep 1;
    }
[download]

it all works out.

Adding use Devel::Peek and Dump [$t, $message, $result]; to the original loop shows some other interesting results:

SV = IV(0x1a65bf8) at 0x1a65c08
  REFCNT = 1
  FLAGS = (TEMP,ROK)
  RV = 0x1a65cb0
  SV = PVAV(0x1a54f50) at 0x1a65cb0
    REFCNT = 1
    FLAGS = ()
    ARRAY = 0x19b75a0
    FILL = 2
    MAX = 2
    ARYLEN = 0x0
    FLAGS = (REAL)
    Elt No. 0
    SV = PVNV(0x1a10e10) at 0x1a65d58
      REFCNT = 1
      FLAGS = (IOK,pIOK)
      IV = 8
      NV = 0
      PV = 0
    Elt No. 1
    SV = PVNV(0x1a5eda0) at 0x19a6a60
      REFCNT = 1
      FLAGS = (POK,pIOK,pNOK,pPOK)
      IV = 1
      NV = 1
      PV = 0x1a2c2b0 "2\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\
+0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0
+\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\
+0\0\0\0\0\0"\0
      CUR = 99
      LEN = 104
    Elt No. 2
    SV = PVNV(0x1a5edc0) at 0x1a65770
      REFCNT = 1
      FLAGS = (NOK,POK,pNOK,pPOK)
      IV = 0
      NV = 6
      PV = 0x1a37f80 "6"\0
      CUR = 1
      LEN = 16
8 - 2 is 7
[download]

So, lots of trailing \0's in $message. Not sure how that leads to the disconnect between IV/NV and PV though.

Update: removing the \0's seems to fix it too:

$message =~ s/\0+//g;
[download]