I could be completely wrong, but 40:96 (& 40:97) are BIOS data and DOS would not normally have any direct effect on them. The enhanced keyboard bit should be set (or not) by the BIOS before DOS (or any OS) even begins to boot. Some of the bits will change in real-time as keys are being pressed and released (and the BIOS is managing the keyboard), but the enhanced keyboard ID bit should never change after the BIOS has configured it at boot time.
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