Mobo is: Intel D945GCLF Little Falls Iv'e try'd mkinitrd with mounted /sys, /proc and /dev from the live cd without any special parameters, so my think was, sata is visible and should be enabled by default. The LVM is not longer included in the new initrd because the lvm messages are gone on booting kernel.
I'd say that's your problem there :) Add a --preload and load the applicable module based on how your bios is set up. If it can do AHCI, and I think it can, use that.
Not sure how mkinitrd works from a livecd when your modprobe.conf is on the "rescued" system. Maybe running from a chroot might overcome any ambiguity, but you most likely don't have an appropriate modprobe.conf on the dead system that is even right.
--preload will force it in where it needs to be. You need some combination of ahci, ata_piix and libata. Someone the wiser chime in. Those are what are applicable to this mobo under any possible config, it's an ICH7 board.
jlc