Re boot; I suspect the boot sector has some 286 instructions on it, as 
it was probably formatted under Windows NT based OS. You can clear it 
all away with my wipedisk utility (note, you need to press upper-case C 
to clear it):

wiki: http://www.lo-tech.co.uk/wiki/WipeDisk
exe:  http://www.lo-tech.co.uk/downloads/utils/WIPEDISK.zip

Command: wipedisk, then upper-case C, then reboot from floppy and 
fdisk/format in the usual way.

Next, I suspect you're using an old version of xtcfmode and possibly 
the BIOS as well. Try flashing the BIOS using this:

exe: 
http://www.lo-tech.co.uk/downloads/XT-IDE/lo-tech-Flash-utility.zip
bin: 
http://www.lo-tech.co.uk/downloads/XT-IDE/lo-tech-isa-compactflash-adapter/xtide-r566-xt-cf-master-slave.zip

Command: flash ide_xt.bin d000, then reboot

Then, use this version of XTCFMODE:

wiki: http://www.lo-tech.co.uk/wiki/XTCFMODE
exe:  http://www.lo-tech.co.uk/downloads/XT-CF/XTCFMODE.zip

Command for DMA: xtcfmode 80 set 2


That all sounds much worse than it is... only probably 5 to 10 mins to 
get everything up and running :)

Cheers!
James.