This is what manual says about the save system:
This save allows you to start at the beginning of the level you were on when you saved.
A checkpoint in the middle of the longest missions enables you to go back to this point if you die in the second part of the mission.
The save system is indeed broken.
It sometimes not even save between missions, not only checkpoints.
I finished mission 4 or 5, where you are on the roof and use your hook for the first time.
Then new mission started on some snowy location (island or somewhere), I made save and F5 like always to be safe and took a break.
Yes, when I loaded, I am again at the beginning of previous mission.
Whats more, no matter what resolution I set, even if it says 1600x1200 in settings, it keeps displaying 1024x768 in practice.
I like the game and I play a lot of retro since 90s, but I am done with this title, since I do not want to waste my time on repeating same levels I already finished over and over due to some broken save system (I never seen such BS in other, even much older games).