The primary DOS usually C: meeds to be active for the OS to recognize it.
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DOS doesn't require that. Some buggy BIOS'es do. The BIOS is simply supposed to read the first physical sector from the floppy, then if it doesn't exist, the hard drive. A few BIOS'es check the partition table on the hard drive to see if there is an active partition before continuing. The BIOS should know nothing about the partition table. It is simply supposed to read the first sector. Then the boot loader reads the partition table.
If the partitions show-up under fdisk (but not as drives under DOS), then sometimes running "fdisk /mbr" will fix it. That recreates the master boot record. Simply running fdisk does not recreate this. I don't think this will fix it, but it's worth a try. It's also something nice to try to fix things after getting a virus (they sometimes infect the boot record) or installing a different boot manager.z