I don't mean to pile on, but... what are you
doing?
When you die, pick "Retry", not "Retry from last checkpoint". Checkpoint saves are kind of like a "backup" save, they are created when resting at the inn
or using a Rift Stone. It's a separate save from your main save (which is both the normal Auto-Save like when you complete a quest or enter a room/area/loading screen, and your manual saves which override each others).
If you manually save often, and hit Retry when you die, you will reload at your manual save. If you pick "Reload from checkpoint", you will respawn at the last inn or riftstone you used, which may or may not be quite a long time ago.
I don't know what you mean by "physical checkpoints". You should re-appear exactly where you hit "Save and continue" if you die. Literally exactly at the same physical space. If this doesn't happen, something is wrong with your computer..
...Which might very well be because the problems you describe are frankly a bit alarming and not at all expected. Even if Dragon's Dogma is the only game that causes you these troubles, they are not normal by any means and as LurkerPrime said, you should definitely investigate and troubleshoot this before continuing.