I'm mobile at the moment, so can't test further right now. However, a few things. Calling pp with -vvv this enables the highest level of verbose output. With the -L flag, provided with a file name this becomes the log for output, rather that stdout. See the documentation for various options. You could enable logging to discover the packaging process, compare the process for the different options and track down the reason from there. Similarly, extracting each exe into a directory will allow you to explore and compare the output. Comparing logs is probably easier :)
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