I haven't used Windows partition since mid-June and I booted the system once again just a few days ago. My first action was as usual update all programs marked to be updated (including Windows updates). Today MSE detected TrojanDownloader:Win32/Tugspay.A in chrome directory, which I believe to be for persistent storage after Googling. Since only option was to remove or leave it - I removed the file.
I run a full MSE scan but nothing has been shown up. When I booted computer from AVG LiveUSB (created on different computer and inserted after shutdown) it did not detect anything except cookies and adware in recycle bin (after checking - some time ago 'Download Manager' tried to be downloaded on my computer and I deleted it without running).
Should I believe that malware was put into persistent storage but has not been run, perform any extra security steps to check it or reinstall the Windows (the last step is relatively expensive for me in terms of time/hassle - it's a private computer so there isn't anything like remote deploy system etc.).