Well, Amithlon scratches the HDD no matter how many buffers you set up. It's probably an issue of the underlying Linux.
The stack size for file system programs can be set in the RDB (just like in a mount list). But AFAIK HDToolbox does not offer the option to edit it. Try HDInsttools from Aminet, I've heared it can edit the stack size. Or write your own program to patch the RDB.
Bye,
Thomas