Wait, are there any patches or mods that affect save files in Resident Evil 4? Probably not relevant here, but just to be sure. No, the focus is on the basic save functionality.
Double-checking the PCSX2 documentation might be useful to confirm the memory card settings. Also, looking up any Resident Evil 4 specific threads in PCSX2 forums or Reddit to see if there are known save issues. It seems unlikely that there's a widespread problem, but better safe than sorry. resident evil 4 pcsx2 memory card save file best
(PCSX2: PS2 Emulator for PC)