My Linux box does not turn off when I run poweroff. It is a Compaq Presario 6000. The logs clearly show that acpi_power_off is called at the end of the shutdown process, but the computer simply hangs showing the shell as it was after the shutdown process until I press the power button on the front of the tower manually. How can I fix this? It's very annoying to have to get up to turn it off every time...

I did notice a setting in the BIOS titled "ACPI/USB Buffers At Top Of Memory", but setting it trashed GRUB, probably by overwriting the MBR. I didn't want to set it and reinstall GRUB before I was sure it'd help though. What does this setting do?

Which Linux?
It probably is an ACPI setting in the operating system, if power off worked on this box before with another operating system, there should be no need to touch anything in the bios.