I had to restart my game due to a hard drive crash and paused the first game day before yesterday, with 9 villagers, knowing that I was going to be too busy to check on them. When I continued the game, I had 3 villagers dead, the remainder sick or extremely weakened. None were where I left them, the fire was out, and there were corpses scattered about.

Does pause not work as intended?

What a terrible tragedy! Did you pause the game and leave it on the Menu screen? If so, I've read that the pause will not work in that instance. If you exited out of the game, then I don't know. In case you don't know, you can pause and unpause by hitting the spacebar. I generally pause the game this way before exiting out to be assured the game is really paused.

I paused the game with the spacebar and exited the game completely. I do leave the machine running 24/7 unless there's a risk of bad weather or I'm leaving for an extended period of time.

I've been playing with it since and have noticed, with other tribes - if I place villagers in specific spots, pause the game and close it, then come back later, my villagers have moved significantly, even going back to a task.

Yes, after you return to a game, the villagers are sometimes in different places. That is normal but since you paused it, nothing should have happened and they shouldn't have died.

Pause does not record your villager's last location; the game, when opened, simply calculates things like the amount of work done since they were last saved. Even when paused properly, they won't load up in the same places.

Did you shut down properly, or close it via windows commands? (The red 'x' in windowed mode, or right clicking the taskbar to close) If it doesn't shut down properly, and didn't auto-save progress before you closed it, it may not have been recorded.

I pause, then exit. The game is still showing as paused when I reopen it.

That is weird. I pause my game quite often when I'm completing a puzzle to make sure villagers stay on task. You may want to post something in the bugs section.