The buttons in question are the difficulty select buttons and the fire buttons.
Since P1 Start isn't one of those buttons, that probably rules out IPac shifted functions.
According to the Daphne wiki
Input page, the keystrokes for the functions that are causing the problem are probably "L.Ctrl" for fire, "/ (keypad)" for Cadet skill level, "* (keypad)" for Captain skill level, and "- (keypad)" for Space Ace skill level.
Assuming that the fire buttons are both connected to IPac port 1SW1 which outputs the default "L.Ctrl", that raises the possibility that you're loking at some obscure (customized?) Windows hotkey combo, a program called 3RVX, or an AutoHotKey script.
https://www.alphr.com/adjust-audio-hotkeys-windows/Try moving the fire button input wires from input 1SW1 (L.Ctrl) to 1SW3 (Space Bar)
or reprogramming your fire button 1SW1 input from "L.Ctrl" to "Space Bar" since that is mentioned as an alternate control in the wiki.
- With any luck, you won't even need to make any changes in DaphneLoader or edit the dapinput.ini file.
https://www.daphne-emu.com:9443/mediawiki/index.php/InputScott