It seems like this problem has to do with the refresh rate. Monitors require different refresh rates depending on the resolution you wish to use. Check your monitor's manual (or search for your monitor model on the web) to find the refresh rate for 640x480 resolution.
In windows, go into Display Properties, then the Settings tab, then Advanced, then the Monitor tab where you can change the refresh frequency to a lower value (for a lower resolution).
You said this started happening when you caught a virus? The virus may have left nasty remnants of its existance or even might not be fully destroyed from your system.
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