Hi Kurt,
if you run a command line interpreter from an application that is running in x86 mode (32-bit processing) then the 32-bit interpreter is executed. In SetupBuilder, you can use the "Set x64 mode..." script function to switch the setup application (at runtime) into 64-bit processing mode. See attached screenshot. After doing this, the setup will execute the 64-bit interpreter. Don't forget to disable x64 mode!
Does this help?
Friedrich