I had the same issue with my old 486DX-33 machine. It would actually work fine with some SD cards I had, but not with any of my CF cards (that are supposed to be less problematic). I made a boot disk with FDISK on it, I created the DOS partition on the CF card with FDISK, formatted it with /s, then ran FDISK /mbr, and then it started booting from it just fine.
I also had a separate issue of the BIOS recognizing the cards properly since it has no auto detection, so I used IDEINFO on a newer computer to determine the numbers to be entered.
I would make the partition slightly smaller, around 500 MB. Originally, I made the mistake of having a 1 GB FAT16 partition. DOS 6.22 and Windows 3.11 seemingly recognized it, but refused to write on or read from a big chunk of the partition. Technically DOS 6.22 can handle up to 2 GB FAT16 partitions, but BIOS limitation may cap it at 504 MB, like it was in my case.