Half Speed and Loss of subfolder file access

I bought and installed Acronis True Image about a month ago having tried about six other products. This was the only backup software that would preserve user status files with BigFishGames MahjongTowersEternity. All other cloning or copying software would contaminate those files.
Unfortunately somewhere along the way my computer became infested with 58 malware entities and it took me several days to eliminate them all with multiple cleaner products. Meanwhile Acronis downloaded version 2015 which I disliked because of its confusing user interface and questionable functionality. I uninstalled it and now have reinstalled version 2014.
Now I note that the version 2014 I have now runs about half as fast as before and furthermore, I cannot directly address subfolders on the destination disk to determine their contents as I could before. So in fact I do not have what I had before but am not sure why.

Suggestions will be welcome.

Raymond Zachary