Ah yes, per the default settings, scheduled scans are set for 2AM every day. And like everyone with a computer that uses a decent amount of power that pays their own electricity bill and works full time, my computer is off at 2AM. Those settings seem a bit daft to be defaults. Thank you for the suggestion and I hope this fixes it.
Every single time my computer starts up in Windows 8.1, there is a popup saying "a scheduled scan was missed". I have manually run scans repeatedly and they have finished, but the popup appears every time. Specs: AMD FX-8350 Windows 8.1 64 bit EVGA 780Ti SC 8GB DDR3