It seems the problems have arisen since Microsoft released its latest batch of security updates for its operating systems, ranging across Windows 7, Vista XP, NT and others.
The problem sees users faced with no desktop, task bar, system tray or sidebar, just a black screen and a solitary My Computer Explorer window.
The company said in a statement: "Microsoft is investigating reports that its latest release of security updates is resulting in system issues for some customers.”
"Once we complete our investigation, we will provide detailed guidance on how to prevent or address these issues."
Software firm Prevx uncovered the problem on its blog, and said that “millions” of people may be affected.
The good news is that while Microsoft beavers away at sorting an official fix, Prevx has listed a step by step work around that could save you having to reboot all the time.
The company has said it won’t work for everyone, but if your problems have begun in the past two weeks after running a Windows update or security program, there’s a good chance it’ll sort it.
If you’ve been affected, check out the short term fix from Prevx and let us know if it works below.