It's not HDToolbox, it is the drive spinning up too slow and spinning down during reset. Do you have Kickstart 3.1 ? If not, get it, it waits longer for the drive to spin up than every older Kickstart.
If you already have Kick 3.1 or don't want to buy it, cut the reset line on the IDE cable (Pin 1, usually the one marked red). Be carefull to not cut any other line. Now the drive may still be invisible after power-up but should appear during warm-reset and not disappear again until you switch off the computer.
However, if you still want to try another partitioning program, get HDInstTool from Aminet.
http://de.aminet.net/aminetbin/find?hdinsttoolBye,
Thomas
