NPE doesn't fix command altered by virus on reboot

I had a rogue 'Window 7 virus protection' malware installed in my computer after I think I clicked on a masqueraded update for the adobe flash software. I have met with similar versions of the virus numerous times already (to my annoyance), But this time the virus that may have changed a command on my computer from starting several programs on startup; it also included the usual changed file association where every file I open requires me to navigate through the 'open with program' to use them . I was able to get NPE to work, which helped me numerous times for similar occurences of the virus, but this time when NPE makes me reboot so it can fix the commands on the next system startup it wouldn't open. No matter how many times I tried NPE it wouldn't function properly on the restart to successfully make the fixes. I'm a computer illiterate and don't know how to work with command scripts and the such, so can someone tell me how I can change the altered commands on the system settings?