Super Puzzle Fighter II Turbo HD Remix [NPUB30017]

Very good, with the "fixes Cellpad # 257", the pad handler enabled, the game runs without any previous errors!

However, it does not recognize the buttons when it asks to press the start button.

Try pressing several buttons at the same time, or keeping some button continuously pressed down while pressing another. Basically, mash the keyboard and see if something happens

I tried to do as you recommended and still does not recognize the commands. It seems that fixing the problem turned to skip the controller during boot in order to not interrupt the progress!
I believe that the start button was recognized there was a certain chance of advancing to the screen for selecting the characters, noting that freezing the game occurs when viewing this presentation.
Is observed in the log file then the "Unknown syscall: 880-00000370 and Unknown syscall: 880-00000371" errors followed by Read32 error and following the crash of emulation occurs.