I just went into the boot menu and did not find a setting to enable or disable the onboard IDE.
It's called SCSI patch in the System menu.
You should do a flash update, even if you already have the latest flash, just to reset all options to default. Also the flash update archive contains documentation of the bios menu.
http://powerup.amigaworld.de/index.php?lang=en&page=13Bye,
Thomas