I am using knoppix 3.8

I continually get an error that seems to be preventing me from loading the system configuration, I am fairly certain that this may mean that the configuration file is corrupted but I am not certain, I use the drive containing the configuration file with both windows and knoppix, does this increase the probability of the files being corrupt? Is there a way for me to prevent corruption on a drive that I use with both knoppix and windows, what about using the drive with both knoppix and windows makes it more likely to corrupt the configuration file? I'm still a newb here and am unlikely to figure this one out for myself, so any help would be much appreciated