@valdasta, there’s so much malware out there for Windows, the attack vectors at their disposal are so varied, and Windows security architecture is so poor that it’s almost a practical impossibility for you to determine with 100% certainty if your system has been compromised.
You cannot trust anti-virus scanner software. First of all, no single anti-virus utility can detect all known (let alone unknown) malware signatures. You must use 2, 3, or more. Second, and perhaps most important, some of the more elegant malware attacks specifically block the anti-virus scanner’s ability to work which allows them to hide and continue operations.
In my experience and observations, the only sure-fire way to have a clean system is to reformat the hard drive, re-install the OS with all the latest patches, and then re-install your trusted applications. And then you’ll want to carefully re-introduce data files in case they have any unwanted hitchhiker malware.
BTW, for your original question – assuming there’s zero malware on your machine – you might just have some conflicting files, partial installs, whatever. The fix for that would be the same: reformat and reinstall.
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Of course, that’s way too cumbersome to deal with on a regular basis, even if only once a year. So, most of us who are afflicted with running Windows everyday just take the normal countermeasures (anti-virus + frequent patches + be careful what you download) and hope for the best, replacing our system every couple of years or so.