The problem, which has caused users to see a completely black screen after logging on, was identified by British software security firm Prevx last week, and received widespread attention after a report by the BBC yesterday.
Prevx had claimed that changes to Microsoft's operating system's registry — the database that stores configuration settings — were the most likely cause of the error, but Microsoft denied that.
"Microsoft has investigated reports that its November security updates made changes to permissions in the registry that are resulting in system issues for some customers," Microsoft representative Christopher Budd said.
"The company has found those reports to be inaccurate and our comprehensive investigation has shown that none of the recently released updates are related to the behavior described in the reports."
He added that Microsoft's support teams were not seeing this as a big issue for users, but urged Microsoft customers to contact support for free assistance in the event of problems.