What motherboard do you have?
What interface the keyboard has?
Do you have alternate Num Pad Keys (17 Keys Section) on the right side of the keyboard?
If yes, did you try operating those keys e.g. DEL on Alternate Numeric Keypad?
The problem might lie in certain Firmware (BIOS/UEFI) Settings on your board. You may need to experiment with that. e.g. USB Settings, SATA/IDE Mode settings, Num Lock Seek at boot , BIOS Shadow settings etc.
Did you try connecting the board to alternate port on your PC?
Are you using any USB Hubs? If yes, remove.
Did you discover this behavior by chance or was it working before?
A somewhat risky option is to check if the board has any updates to UEFI/BIOS and if yes try to flash he BIOS to latest version and check also. I assume you are familiar with such procedures.