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Let's go through this in detail
1. Grub shows a screen, & you select something.
2. That kernel is loaded, usually from /boot
3. That kernel boots.
4. That kernel mounts the root filesystem specified by 'root=' on the command line read only
5. It then goes looking for /sbin/init on the root directory
6. Init starts up.
At which exact point does it barf? A number, please.
Well, the usual error there is: "Unable to mount root fs" or something like that.
Inappropriate IOCTL makes me think the device is being addressed the wrong way - like looking for the ignition key on your horse, or the reins in your car. :-). Google tells me it's a common enough disk error. The difference between reading the disk in 2. & 4. is that 2. is started by the bios but 4. is done by the kernel, so the kernel has to be capable of reading the disk.
Check that kernel .config. If it is ok, run
make clean && make > make.err 2>&1
without any parallel builds, and you can check if the 2 kernels are the same with md5sum. Read over make.err and check for errors - ignore warnings. It's probably a m/b chipset error, or a driver error, or a driver/chipset problem. Read the help.