Usually what the linker is outputting is not an issue as it gets loaded into eprom but I can understand where you might have an issue. The reason you read back different data is that the areas that aren't filled in by the intel hex data remain at whatever value they were set at previously - I assume this is the problem you are reporting. Anyway, one method is to use two utilities : hextobin and bintohex (do a search with google) - hextobin does what it says:takes in a intel hex file and creates a bin file. bintohex does the opposite: takes a bin file and creates a hex file. In doing this the output is a intel hex file that is contiguous.