The most common reason for those keyboard related issues is that you are using a configuration with one of the joystick keyboard replacements being active at one of the gameports. I am quite confident the problem is related to this. Please note that while keyboard layout 1 does use mostly the cursor keys, it also has O and P being used for autofire.
Which keys exactly are not working, can you give some example what configuration you are using and which keys exactly aren't working?
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