Today I did a full system scan and Avast said some files could not be scanned, these included Adobe Flash install files in my download files which aren’t there. So I did another scan and they did not appear, but on the 3rd time these files were scanned again despite them not being there. Any help would be appreciated.
It could just be possible adobe temp files… (adobe updater runs in background etc). Not to worry about.
I don’t think it is because when I scan downloads folder by itself, it gets some files could not be scanned and shows folders in Windows\WinSxS and Skydrive folders. It also says a file or dictionary is corrupted, despite the fact I have repaired this file and doing another Chkdsk it says there is no problems. It seems to be showing random results from past scans in the scan you do.
We get this question (variations of the same) a lot.
Files “that can’t be scanned” are most often just that: Files that can’t be scanned; ‘protected files’ of other software programs you have installed.
Many software programs protect their files. (Adobe is one such software).
I would not sweat the small stuff.
I had this happen with a skype installer or flash player installer before where it said it wasn’t scannable and was told that if I rebooted and scanned again it would show up as nothing… and the next time I scanned after a reboot it came up with no issues. It does seem to happen on installer files a fair bit from the frequency I’ve seen people ask on here.
So why when I do a right click and scan the Downloads folder by its self am I getting results from Skydrive and Windows\winSxS when these folders have nothing to do with the downloads folder.
Why are you scanning the download folder? ???
Since most, if not all, files in the download file are not executable
you are wasting your time. Once those files are accessed the file shield
will then scan them. FYI I run a quick scan once a week when I know my laptop
will be in use and a full scan once a week. 
I know that, I was scanning it because it said the un scannable files were in there so I did a scan of that folder separately and the results kept changing and displaying things that weren’t in that folder.