Wait a second are you using my method??? How did you determine your nand is not correct, hex editor or fc command???
What type of cable setup do you have, did you use an rj45 cable? One more thing, NandCompare is a last ditch effort and should never be use in place of actually dumping two matching dump. You need to be able to dump at least two to three matching dumps. NandCompare is suppose to be for those people that have erased their nand and have no other methods of getting the original. Don't use NandCompare to avoid doing a job right because your just going to end up with a brick.
Can you list your bad blocks or programming errors.
Can you take a quick picture of your cable setup and share....
PS from my personal experience, my first dump never match my second. But my second, third, fourth, fifth, sixth and seventh all match.
to make the dump quicker try the following if your using my tutorial..
nandpro lpt: -r256 c1.bin 0 75
nandpro lpt: -r256 c2.bin 0 75
nandpro lpt: -r256 c3.bin 0 75
nandpro lpt: -r256 c4.bin 0 75
compare those files and get back to me...