Sounds like you have an issue with the floppy controller not accepting the BIOS setting of a 1.44 drive when a HD is connected. What exact motherboard, what exact floppy controller AND what exact floppy drive (makes and models of each please)? Also are you using the end of the floppy cable (after the twist) AND what real HD have you tried ? Won't bug you about it but as a reminder: anyone messing with old hardware should always have a spare working part for everything they are working with if they really want to enjoy this hobby and not get too frustrated 😁

null

I had a very similar problem with a machine one time. Ended up being the CF card believe it or not. Switched to a different brand and problem went away.

null

What type of battery did you use to replace the barrel type ? If the original barrel type was rechargeable through the board
then not using a blocking diode on a non-rechargable cell would cause problems with the power to the CMOS chip.
Sounds like the CMOS chip was resetting on each boot of the machine. Sometimes you should fully power off the system
when changing the BIOS settings.

Maybe the new battery has lower voltage then the original and it is sinking the power supply to the CMOS chip below it’s operating voltage. But that would only be the case if it was connected to the original barrel battery leads/solder pads.