I think the issue is probably in using pure python, we use it a lot, somewhat ignoring Ren'Py - the system trigger scene uses just pure python, no Ren'Py scripting. That's probably the main cause. But we aren't just throwing the idea of save compatibility into the trash and might one day fix it. It's hard enough to fix, so we still haven't found a solution. We have to put up with this fact, but we're trying to make more checkpoints for easy loading - another one is coming soon. I also recommend the force skip function, then you'll get to the scene you want faster.
