USB booting :: files disappearing

i'm not sure if this topic should be under hd-install or here..
i've installed DSL on my cf card (got a cf card adapter onboard and the system reckognizes it as hdc) but i managed to do it only when i did usb install and chose hdc1 as the usb drive, now DSL boots fine, started remastering the KNOPPIX file to include all the apps i need. what irks me is this: whenever i do some change to the cf card's content (mounted RW as /cdrom) like changing a file in a directory not related to DSL, the changes are gone if i don't do a proper shutdown, now this system is not supposed to be doing a proper shutdown at all once i've configured it properly but just lose power suddenly whenever the device it's in is shutdown. how can i make DSL keep it's hands off that directory?

original here.