Hint: try another USB port.

USB is like a network, and it could be a jungle of cables and ports and switches and bridges and whatnot. But the closer you get to the mainboard, the better are your chances to escape such a problem.

I had an issue where one keyboard (worked with another one) worked in bootloader, but not when entering the encryption password after that. I believe I solved that by moving keyboard earlier in the module list in mkinitcpio.conf. Maybe something similar would solve your issue?

I had a motherboard like this: the USB ports didn't work until it booted into an OS. You had to connect a PS2 to make changes in the BIOS, and could only boot from IDE. It was super-annoying.

Check if you find anything about this in the kernel log (dmesg).

Are you using the usb ports on the motherboard itself? Because you need to with a lot of MBs depending on when they initialize other USB

...on which hardware?

Last i encountered this issue i had to connect it directly to an USB port, instead of through an USB hub.

I believe this is a hardware issue. Have you checked the USB options in the BIOS?

I've had this happen before on some weird systems. Unplugging and replugging the keyboard woke the keyboard back up.

Was there no option about it on the BIOS/UEFI about something like that?