Like others in this thread I've tried everything listed on multiple treads and none of it's worked. I did how ever figure out for me what works.
I did not uninstall my games at all.
I uninstalled Origin and wiped out as much as I could from my harddrive of it's other installed locations on Win7 Ultimate 64bit. cleaned as much of the windows 7 registry as I could and rebooted.
I then got a fresh copy of Origin from the website, installed it, set it up how I wanted, and pointed it to my games.
Tried Dead Space 3 and "Origin in Game" Did not work, updated to beta, still didn't work, downgraded to the normal Origin which made the in game overlay still not work, and finally disabled MSI afterburner and boom now it works.
What sucks for me is I like to monitor my video cards etc and yet again Origin screws that up for me. I never have this problem with Steam at all.
I also remember having the same problem when Mass Effect 3 came out and had to get the IGO32.dll EA had linked somewhere when that came out to get this in game overlay to work and lo and behold this trick still works with Dead Space 3.
TL : DR
1.Disable all of these programs because the overlay doesn't work with them.
https://help.ea.com/article/origin-crashing-during-mass-effect-3
or
2. See this thread
http://forum.ea.com/eaforum/posts/list/8841699.page
or download the IGO32.DLL here
http://www.mediafire.com/download/3yzfln137ra11hs/IGO32.dll
then
Exit Origin
delete or rename the existing IGO32.dll in the Origin Client Directory (Default for windows is C:\Program Files (x86)\Origin ) to something like IGO32.old
download the IGO32.DLL from the mediafire link and move it to the Origin Client Directory where ever you have that located. I would suggest making a backup copy of the file from mediafire since you'll most likely have to replace it when ever EA Updates Origin.
Start up Origin and then "Origin In Game" should work again when you start up Dead Space 3 and who knows you'll possibly be able to use MSI Afterburner or another program with it.
This proves once again that Origin/EA is the problem and that in the barely 2 years Origin has been around that it still has a long way to go before people can even rely on it.
Now if only buying resources with rations worked.
9-7-2013 EDIT: I forgot the resource packs that you use ration seals for are only sold at the bench in game and not in the DLC menu at the main menu.