if it helps, this about drove me mad at first too...
Finally I ended up doing this: (and it worked)
kill it, pull the power and batt, hit the reset for 5+ secs
1) flash as instructed by the docs---
use the nand utils to change 64 meg limit
REBOOT
kill it, pull the power and batt, hit the reset for 5+ secs
REBOOT
2)use nand tools to repartition the nand ( I used 96..though the docs say 58 is good)
REBOOT
kill it, pull the power and batt, hit the reset for 5+ secs
3).Flash (install new system)
reboot from menu
If you use hostap, now would be a good time to install it to flash ( I suffered some confusion on hostap installation and found this works well-- doing it right off before any new weirdness causes installation problems)
I unmounted all hd partitions and ran cfdisk /dev/hda
put partition2 as swap ( I use @128M) at beginning of drive
By putting partition 1 at the end of the drive
This way, pdaxrom automatically mounts /dev/hda1 as /mnt/ide and links on reboot, and swap is on the "fastest" part of the drive
I've been doing the swap manually (1 instance of mksap /dev/hda2 then swapon or swapoff /dev/hda when wanted. ) I'm sure it can be done automatically.. just haven't pursued it
reboot... and all should be well.
1 BIG warning though.... for some reason mine prefers the external to the internal cf as hda. That is to say that if you have a cf card or drive in your external slot on rebooting (not coming out of suspend, that works fine) then it will tend to mount that external card as /mnt/ide and give you a nasty surprise. No damage is done, however and rebooting without a data device in the external slot brings everything back to normal