This is not an amnesia issue only, it occurs to other games too. Had that problem with a game (don't remember the name though) and that game should run fine on my computer. I guess its a steam issue, or some files been corrupt in the game after reboot. Try the verify "integrity of game cache" function on steam, you can find it if you right-click on amnesia and choose "properties" "Local Files" Tab and there you go.
If that doesn't help you can try what "Spooder Wekd" said. Re-install steam and then try.
Oh yeah now i remember what game it was... It was actually Counter-Strike 1.6 believe it or not haha *smirk*
I fixed it with re-installing steam after i verified the cache!
BUT if that still doesn't work, i have no clue actually. Maybe try update your graphics card or directX. I know it's not the issue, but it is always worth a shot.
It could also happend that if you didn't reboot correctly (like shutting it off by holding in the powerbutton) it could corrupt the files, because sometimes the system saves the info after reboot, and by shutting it off in the wrong way could cause the system reg not to store the info of the game. (I'm not that of an expert and may be totally wrong haha but im atlest trying to come up with solutions that could work)
I checked the hpl.log now and i can clearly see that there is some issues loading a lot of files in the game due to missing files.
Maybe there is your answer? So i think "Verify integrity of game chache" SHOULD fix the whole thing, because it searches and finds the corrupt/missing files, downloads it and installs it.
Hope this works