Windows 7 Application Not Found Error

I recently had a virus-esque program on my computer called win 7 home security 2011. It was a fake anti-virus program that was telling me I had viruses in an attempt to get me to buy their fake product. Anyway, the program is now history but I am encountering more problems that may or may not be a side effect of the virus. When I try to open an application I get an error giving the file location of the application followed by the message "Application not found". I can get around this and open the application by following the file location given by the error message and opening it. It then forces me to choose which program to open it with, in which case I need to tell it to open it with itself...

This is very irritating and in many cases makes opening applications close to impossible. When I'm choosing the program to open it with, it won't allow me to check the box telling it to set the program as the default. Is there any way to solve this issue short of completely re-installing windows 7?