system32 / systemwow64 folders are "virtual" in the sense that their contents are determined by the OS depending on the access application bit - in your case cmd.exe is probably a 64-bit version, so it will always run a 64 bit version of the mshta file. exe
to run the command line in 32 bits see http://astatalk.com/thread/7382/0/How_to_Open_and_Run_32-bit_Command_Prompt_in_x64_Windows/
it can also help to use SysNative instead of system32 and see how mshta.exe works ...
mshata.exe apparently just uses the standard settings for .hta, so it probably doesn't matter if you are starting the 32-bit or 64-bit version of mshta.exe - you can try linking .hta with 32- bit transfer your browser ...
IF you want to get around this, then you can just call the browser (32 bit or 64 bit) directly in your batch file ...
EDIT - as per the comment:
For 64 bit execution you can use "C: \ Program Files \ Internet Explorer \ iexplore.exe" in your batch file and
for 32-bit execution you use "C: \ Program Files (x86) \ Internet Explorer \ iexplore.exe".
Depending on the youd system, you need to open a command shell with the desired bit size - see the link above.
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