With serial drivers one always worries about overruns and framing errors. These are usually the reason for lost data. Probably also the reason sysread is choking. I would expect to see some error handling in your read loop but I don't see any. Something like: (From the manual)

 ($BlockingFlags, $InBytes, $OutBytes, $LatchErrorFlags) = $PortObj->i
+s_status
        || warn "could not get port status\n";

  $ClearedErrorFlags = $PortObj->reset_error;
        # The API resets errors when reading status, $LatchErrorFlags
        # is all $ErrorFlags since they were last explicitly cleared

  if ($BlockingFlags) { warn "Port is blocked"; }
  if ($BlockingFlags & BM_fCtsHold) { warn "Waiting for CTS"; }
  if ($LatchErrorFlags & CE_FRAME) { warn "Framing Error"; }
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Does your device implement rts/cts flow control? Does the serial cable contain the rts/cts lines. Do any adapters omit those lines?