I might have had the exact same problem as you: https://forums.factorio.com/viewtopic.php?f=7&t=55059

Check you VRAM usage. It is probably maxed out causing excessive swapping to main memory.

My 3GB card does not have enough storage for high res sprites and VRAM usage "All". You need 4GB at least ...

The only thing that I do notice is that this part from a normal shutdown is missing:

(previous log stopped here with DSound: Deallocated voice)
95.643 Steam API shutdown. <--
95.661 Goodbye <--

I am running this Steam version: https://imgur.com/Bc73cOi

Today after exiting Factorio in an attempt to get some sleep I got the following error:

Factorio has stopped working
...
Problem signature:
Problem Event Name: BEX64
Application Name: Factorio.exe
Application Version: 0.16.6.34439
Application Timestamp: 5a37f6ac
Fault Module Name: d3d9.dll ...

I reduced VRAM usage from "All" to "High" which seems to have solved the problem.

What does "High" mean in this case? Does it mean "use 2GB" or some percentage of total space?

I checked VRAM usage and you are right. It quickly shoots up to 2.9 GB which is a sad fact. I should have bought the 6 GB edition four years ago.

Will try reducing the VRAM usage option.

I would suggest two things (there's probably a different subforum for this):
1) Estimate VRAM usage as a ...

Since Factorio version 0.16.1 (up to 0.16.3) on my machine the game does not quite reach 60 FPS anymore and hickups/stalls for a few hundred ms(?) about once every two seconds. The FPS counter shows periods of nice 59.9 or 60 FPS and brief periods of 55~59 FPS in between. For the stall behaviour it ...