I'm running fedora core 5 and currently it's loading the ata_piix module for my sata controller. This module is causing the machine to lock up and so I need to load the ahci module instead. Both modules depend on the libata module.

In /etc/modprobe.conf i've set
"alias scsi_hostadapter" from ata_piix to ahci

I've also enter
install scsi_hostadapter /sbin/modprobe ahci
and
remove ata_piix /sbin/modprobe -r ata_piix

but it still boots with ata_piix loaded and not ahci.

Why?

Try adding:
to your /etc/modprobe.conf.

I did what you said but still nothing, I also added

blacklist ata_piix

to

/etc/modprobe.d/blacklist

anymore ideas?

Aha, didn't know if fedora had a separate blacklist file. If it has one, best to put it in there.

I really should collect virtual machines of all major distros before I reply

Perhaps this module is required by another. Doing lsmod will show deps, e.g. I have a line in my lsmod output:
Which shows that the snd_ac87_codec is dependent on snd_intex8x0. Do lsmod and grrep for ata_piix:
and see if it is being loaded as a dependency. blacklist anything which depends on this module too. I'm not sure how the blacklisting works, but maybe it still loads modules indirectly. Can anyone clarify this?