In any case. your tool worked well with Ruby @I_inject_crayons you can use pokecal's tool for Ruby. (Usable data exist, but somehow the header is somehow corrupted, hence not readable by VBA or PKHeX)
We cannot extract usable data, if usable data doesn't exist (and that's similar to the response to 'can't we just edit the numbers' I gave you in the other thread).
Programs don't just perform magic, ya know
As for FireRed and Emerald, it looks like junk data. Take photographs of your carts (and put the photographs in a spoiler), and we can confirm if they are real or fake carts. It's possible that only Sapphire is a legitimate cart. (It's backed up properly and immediately works with PKHeX)
If all your carts were determined to be real, re-download gba backup tool, try a few different versions.
Sometimes using the corrupted backup tool would lead to corrupted saves.