I don't see any checksums (or any data) there in Sapphire or Emerald. If it works like it does in 4th and 5th gen games, there's a block of data with a checksum at the end. Try looking there, or where ever a seemingly random 4 byte sequence follows or precedes data. Change things in game and look for that kind of change. If it's like in Black and White, the checksum may be a CRC16-CCITT. Other users may be able to help you more, but if not, post where you think the checksums are and I'll see chat I can do. For all I know, it could be like Mystery Dungeon Explorers of Sky (where data is split into 4 byte "words", added together, and part of the result is the checksum).
[Edit] Oh, also look at Pokebox GBA (listed in this thread), because it should be able to fix the checksums for you, helping determine where they are.