If you change the configuration of your hardware to such an extent that it is very different from the original configuration, Windows may flag itself as non-genuine as it uses hardware profiling.
Also for Windows 7, the way to tell if you have a genuine 'Non-genuine' error, you will have this in the bottom corner of the screen:

If not, then it will be some kind of malware.
Also for Windows 7, the way to tell if you have a genuine 'Non-genuine' error, you will have this in the bottom corner of the screen:

If not, then it will be some kind of malware.