IÂ´m not sure I understand you right, but I can see from your post that you are trying to verify "burned data".
As an old Linux user my tool to verify critical data is md5summer. (You never tell us what tools you are using, or how you use them.)
For fun I just made a "real life test".
And this is how I tested and verifyed burned data.
i. I run md5summer on a 233MB ISO-file. (md5 hash-file saved.)
ii. Then I burned the same ISO-file with Nero 188.8.131.52 on a DVD+RW disk (DVD+RW:RICOHJPN-W11-001), as data.
iii. Copied back the burned iso-file to my HDD (another partition) and run md5summer again.
And, you know what... when I run compare in md5summer, the files (data) are exactly the same. Down to the last bit.
OK, IÂ´m a practical man with some knowledge of verifying data. And I donÂ´t care much about NeroÂ´s way of data verification...
I just wanna same data back from my burned DVDÂ´s at that day I need it, as they were originaly. Exactly the same!
Maybe some of our members will be able tell why you get "different" checksums when "comparing" files in your way. I canÂ´t.
You can download md5summer here