What I think you need to do if you're certain they're OK is go to Avast's File System Shield > Settings > Exclusions and add them to the list.
I've had a series of VERY annoying problems like this in recent months since updating to Avast v.8 with it sending stuff to the Virus Chest I know is OK and when you check it in the Virus Chest it reports 'No Virus Found'. You Restore it and then on the next scan or when you come to use that program the problem recurs. My most recent trouble was with the Tomb Raider 4 main .exe, never modified and which has been on my laptop for over two years. It has been scanned by previous Avast versions hundreds of times and at high sensitivity settings without any trouble.
I've now switched off sending stuff automatically to the Virus Chest and changed it to Ask. TR4 now works again without incident.
Strangely I've never had a problem from Avast with the one FTP utility I have on my machine: Auto-Xbins. Not a peep but Malwarebytes flagged it as a trojan the moment it was installed and I had to add it to its Ignore list. That was very much easier to do than Avast's awkward, well hidden add-to exclusion list process. GUI designers take note: simple is good when it comes to this sort of thing.
What you want to be able to do is highlight the file in question and be able to tell Avast to ignore it by adding to the exclusion list. AFAIK the only time you can do this is when the original warning dialogue box appears and if you miss the opportunity it will close and send the suspect file to the Virus Chest. Once there I can see no obvious way for directly adding it to the exclusion list. It's either Restore, Delete, Extract, Scan, send to Virus Lab, Properties, Add (whatever that is meant to do it doesn't take you to the exclusion list) and Refresh. No simple Add to Exclusion list option provided - why not?
