About BootIce info in this scenario let's put it out of the equation, as we both seem to be agree, that for whatever reason, it is giving wrong info on this case.
But nevertheless is good to know it is not trustable on cases like this.
No, it is not "wrong" info, the info is "right", only it is "different info".
The way you see it is because of mis-communication/mis-understandings, seemingly (from your last post) you didn't follow (to the letter) steve6375's instructions:
BootIce does not give a complete picture.
1. Make a 'bad' SD card
2. Run RMPrepUSB - DriveInfo - 0 and save notepad file as BAD0.txt
3. Run RMPrepUSB - DriveInfo - P1 and save notepad file as BADP1.txt
4. Boot it and run geometry --sync (hd0) and quit
5. Run RMPrepUSB - DriveInfo - 0 and save notepad file as SYNC0.txt
6. Run RMPrepUSB - DriveInfo - P1 and save notepad file as SYNCP1.txt
Now you can use WinMerge or similar tool to compare the files.
Please attach 4 files in next post.
If - like you seem to be reporting now, and for any reason - you didn't make step 1, and you used the same SD card where you ALREADY had run geometry --sync, is it so surprising that No differences can be found after re-executing the same command?
What sense has doing steps 2-6 if you didn't do #1?
Why (the heck) did you perform them and post the resulting file? (without specifying that you didn't - because you couldn't or for whatever other reason - perform step #1)?
Now that you cleared that you don't have a reference copy of the thingy when it didn't work but only copies made AFTER the geometry --sync (actually as tinybit correctly stated a geometry --tune followed by a geometry --sync) corrected some values and that as such there is no sense in comparing "before the cure" against "after the cure" because we have not a "before the cure" and we have been (pointlessly) comparing till now "after the cure" against "after the cure", the problem is solved.