just to compare (and again, i am sorry if i misunderstand what you are doing), i build my WIM like this (running from the deployment tools command prompt in the WAIK):
set /p _location= Full Directory where you want to build this (it must not exist already):
copype amd64 %_location%
copy %_location%\winpe.wim c:\%_location%\ISO\sources\boot.wim
dism /mount-wim /wimfile:%_location%\winpe.wim /index:1 /mountdir:c:\winpe\mount
copy c:\bootcd\gimagex.exe c:\winpe\mount\windows\system32\gimagex.exe
xcopy c:\bootcd\Images c:\winpe\mount\Images /y /e /i
xcopy c:\bootcd\scripts c:\winpe\mount\scripts /y /e /i
xcopy c:\bootcd\Ghost64 c:\winpe\mount\windows\Ghost64 /y /e /i
xcopy c:\bootcd\PE_VNC c:\winpe\mount\PE_VNC /y /e /i
xcopy c:\bootcd\startnet.cmd c:\winpe\mount\windows\system32\startnet.cmd /y /e /i
copy c:\bootcd\getmac.exe c:\winpe\mount\windows\system32\getmac.exe
copy c:\bootcd\winpe.bmp c:\winpe\mount\windows\system32\winpe.bmp /y
dism /image:c:\winpe\mount /add-package /packagepath:"C:\program files\windows aik\tools\petools\amd64\winpe_FPs\WinPE-HTA.cab"
dism /image:c:\winpe\mount /add-package /packagepath:"C:\program files\windows aik\tools\petools\amd64\winpe_FPs\WinPE-Scripting.cab"
dism /image:c:\winpe\mount /add-package /packagepath:"C:\program files\windows aik\tools\petools\amd64\winpe_FPs\WinPE-WMI.cab"
<add drivers>
dism /unmount-wim /mountdir:c:\winpe\mount /commit
copy c:\winpe\winpe.wim c:\winpe\ISO\sources\boot.wim /y
SET /p _file= name of file (NO .ISO extension!):
oscdimg -n -bc:\winpe\etfsboot.com c:\winpe\ISO c:\winpe\%_file%.iso