Yes, the patch only patches the RAM of the box. So the changes are lost on reboot or power off.
Thats why a modchip would be a more permanent solution, as it would patch everytime on reboot / power off.
try this...
Remove the hdd, inject a booterce (from the wiki pages) into your NK.BIN file.
replace the NK.BIN on your hdd.
Power up the box, as soon as the hard drive starts to spinm, patch with patcher..
It should now boot with the modded NK.BIN
you can then try to ftp to the box, or http://<insert boxes ip>:8000
replace <insert boxes ip> with the ip of your box.
Mick