Windows 7: Conhost.exe causing windows to lose focus.

I have just started to have an issue with "conhost.exe".
Anytime I have an application running, conhost.exe is running. But after a minute or so the .exe just drops and when it does, whatever window I have up loses focus and I have to click on the window to be able to use it.

I have been on MANY Windows 7 forums trying to find ANYTHING on this "conhost.exe", All i could find is that it is a legitimate command from Microsoft and that it runs under the process "csrss.exe".

Is this just a bug from the new update or is this a product of Malware/virus?

*important notice*
Right before this command started giving me trouble, I somehow got that false FBI virus that locks your computer up until you either pay $200 or get rid of the virus.(I got rid of the virus.)



I have saved a file that shows the processes running on my laptop along with the program to open it up in.(below)
wafflesAutoRuns.zip