Could be a boot priority problem. In HDToolbox, make sure you have access to the Advanced Options in the partitioning window (click the checkbox), and make sure your ~800MB partition is the only one with the "bootable" flag checked. It should have a boot priority of 1.
Since you're using Kickstart 3.1, you should probably get some 3.1 disks - mixing versions could cause some problems. Software Hut, Amigakit, and Vesalia can probably get you some.
EDIT: Might also be a filesystem problem. Make sure there's nothing installed in the RDB and that the partitions are using FFS International Mode (DOS/03).
