Okay, I believe I fixed it. I cannot explain why this works... here is the command history as well as the output. Basically I had to assert DTR low, open the connection, assert DTR high then begin. Any reason why this might be?
EDU>> serialObject = serial('COM4')
     Serial Port Object : Serial-COM4
     Communication Settings 
        Port:               COM4
        BaudRate:           9600
        Terminator:         'LF'
     Communication State 
        Status:             closed
        RecordStatus:       off
     Read/Write State  
        TransferStatus:     idle
        BytesAvailable:     0
        ValuesReceived:     0
        ValuesSent:         0
EDU>> set(serialObject, 'BaudRate', 9600);
set(serialObject, 'Parity', 'none');
set(serialObject, 'ReadASyncMode', 'continuous');
set(serialObject, 'StopBits', 2);
set(serialObject, 'Timeout', 5);
set(serialObject, 'RequestToSend', 'off');
set(serialObject, 'DataTerminalReady', 'off');
set(serialObject, 'FlowControl', 'none');
EDU>> get(serialObject)
    ByteOrder = littleEndian
    BytesAvailable = 0
    BytesAvailableFcn = 
    BytesAvailableFcnCount = 48
    BytesAvailableFcnMode = terminator
    BytesToOutput = 0
    ErrorFcn = 
    InputBufferSize = 512
    Name = Serial-COM4
    ObjectVisibility = on
    OutputBufferSize = 512
    OutputEmptyFcn = 
    RecordDetail = compact
    RecordMode = overwrite
    RecordName = record.txt
    RecordStatus = off
    Status = closed
    Tag = 
    Timeout = 5
    TimerFcn = 
    TimerPeriod = 1
    TransferStatus = idle
    Type = serial
    UserData = []
    ValuesReceived = 0
    ValuesSent = 0
      SERIAL specific properties:
      BaudRate = 9600
      BreakInterruptFcn = 
      DataBits = 8
      DataTerminalReady = off
      FlowControl = none
      Parity = none
      PinStatus = [1x1 struct]
      PinStatusFcn = 
      Port = COM4
      ReadAsyncMode = continuous
      RequestToSend = off
      StopBits = 2
      Terminator = LF
EDU>> fopen(serialObject)
EDU>> get(serialObject)
    ByteOrder = littleEndian
    BytesAvailable = 0
    BytesAvailableFcn = 
    BytesAvailableFcnCount = 48
    BytesAvailableFcnMode = terminator
    BytesToOutput = 0
    ErrorFcn = 
    InputBufferSize = 512
    Name = Serial-COM4
    ObjectVisibility = on
    OutputBufferSize = 512
    OutputEmptyFcn = 
    RecordDetail = compact
    RecordMode = overwrite
    RecordName = record.txt
    RecordStatus = off
    Status = open
    Tag = 
    Timeout = 5
    TimerFcn = 
    TimerPeriod = 1
    TransferStatus = idle
    Type = serial
    UserData = []
    ValuesReceived = 0
    ValuesSent = 0
      SERIAL specific properties:
      BaudRate = 9600
      BreakInterruptFcn = 
      DataBits = 8
      DataTerminalReady = off
      FlowControl = none
      Parity = none
      PinStatus = [1x1 struct]
      PinStatusFcn = 
      Port = COM4
      ReadAsyncMode = continuous
      RequestToSend = off
      StopBits = 2
      Terminator = LF
EDU>> set(serialObject, 'DataTerminalReady', 'on')
EDU>> fprintf(serialObject, '*IDN?')
EDU>> fscanf(serialObject)
ans =
HEWLETT-PACKARD,34401A,0,11-5-2
EDU>> fclose(serialObject)
EDU>> delete(serialObject)






