I've had that problem too, but I discovered a few things.
- If you have replays prior to hacking your brawl, they might desync because of textures or mods.
- Obviously if you change what the stage originally was it will desync.
- Changes in PSA or gameplay.
- Some stages and/or character will cause a desync no matter what.
My solution is not to save that replay. What's the point of saving it if you know it will desync.