Maybe you have low RAM?I didn't have the problem with savegames (yet), but I find it strange that this game has a progress bar when loading a savegame and it takes fucking forever (OK, it's only 12 seconds) to load a save. I've played hundreds of Ren'Py games and most of them were both larger in size and significantly more complex than this game. I can't recall any of them that have had a load progress bar or any of them that took so long to load. They all take only 1 or 2 seconds. Something's amiss with this game.
Edit: Stranger still is that the save file size is only 200-300kB in this game where is it is 2MB-3MB in other games. Yeah, something's amiss.
We didn't have such types of reports, usually it's smth is about 2-4 sec to load, but if you load your system hard - loading can takes more time