Yes, the "w" Nastran executables will attempt to open up a Windows file dialog box which is not compatible with "batch" mode.
As another tip, you can test out the nastran_submit.bat file from the command line. This way you verify that the batch file is set up correctly before launching HyperFEA.
C:\Temp>cd C:\Program Files\HyperSizer\HyperFEA
C:\Program Files\HyperSizer\HyperFEA>nastran_submit.bat "C:\HyperSizer Data\Projects\Collier\_Training UM\RLV\FEA\rlv.dat"
BatchFile: C:\Program Files\HyperSizer\HyperFEA\nastran_submit.bat
FEM Drive : C:
FEM Path : C:\HyperSizer Data\Projects\Collier\_Training UM\RLV\FEA\
FEM FileBase : RLV
FEM Extension: .dat
Full Filename: RLV.dat
NASTRAN : "C:\MSC.Software\MSC_Nastran\20101\bin\Nastran.exe"
MSC.Nastran V2010.1 (Intel Windows XP 5.1 (Build 2600)) Fri Sep 09 09:22:22 2011
*** SYSTEM INFORMATION MESSAGE (pgm: nastran, fn: estimate_job_requirements)
Starting ESTIMATE, please wait...
*** USER INFORMATION MESSAGE (pgm: nastran, fn: estimate_job_requirements)
Estimated DOF=4895
Estimated memory=128.0MB
Estimated disk=23.6MB
Note: ESTIMATE had some difficulty analyzing this job.
MSC.Nastran beginning job rlv.
MSC.Nastran started Fri Sep 9 09:22:23 EDT 2011
MSC.Nastran finished Fri Sep 9 09:22:34 EDT 2011
MSC.Nastran job rlv completed.
C:\HyperSizer Data\Projects\Collier\_Training UM\RLV\FEA>