If your computer has two hard disks on the IDE controller and you are installing MINIX 3 to the second one, sometimes there can be a problem booting. This problem occurs if the second disk does not have a correct boot program in the MBR (Master Boot Record). To solve this problem, boot MINIX 3 from the CD-ROM, log in as root, and type:
installboot -m /dev/c0d1 /usr/mdec/masterboot
This command will install a proper MBR on drive 1 and you should not have any more problems. You may have to reinstall MINIX 3 however.