For any save file with valid checksums, PKHeX can be made to report an invalid checksum by viewing a different box in the "Box" tab. To reproduce:
1. Open any save file with valid checksums in PKHeX.
2. Go to the "SAV" tab and use "Verify Checksums" and/or "Block Data" to see that PKHeX calculates matching checksums upon opening the file.
3. Go to the "Box" tab and view a different box.
4. Repeat step 2 to find that PKHeX now reports problems such as "Large block checksum is invalid" for Gen 4 and "Invalid: 00 @ Region 0000 SAV: 73/74" for Gen 5. This happens even though the data is entirely unchanged to my understanding.
This occurs in ver 221218 for all games I tested from Gen 4, 5, 6 and 7. They are real cartridge save files that I dumped using Checkpoint. Of course, the games load all of these save files with no complaints.
This issue seems low-hanging, so I'm sorry if it's reported already or no one cares.