I'm almost definitely sure that the problem is caused by file permission changes. File permissions changes can be made manually from the 'security' tab of each file or folder, or by other applications or services.
HomeGroup creation changes the file attributes as it allows network users to read some files.
I'm not sure if other programs can make similar changes. Another user in this forum had Nero 2014 installed before the problem appeared.
Other backup applications have similar problems too. Norton's backup feature does the same thing when it detects file permission changes, but it replaces the whole backup instead of making duplicates. Still the same problem though.
On the other hand, Microsoft's SyncToy, a very simple file synchronization utility that can be used for backing up files, is unaffected from this issue. The only actual disadvantaged of the application is that you need to run the backup manually, there is no
schedule or automatic option.