Tim this app is very powerful but if used a certain way it can cause issues due to lack of understanding to what is happening.
If I was in your shoes I would make a full backup and place it in the download folder , I would then delete the app completely and install it fresh then check that my drive has no other backups on it apart from the one in the download folder, before installing the full backup from the download folder, make sure iCloud is turned off , once you have reinstalled the backup check your operating system and ST3 is up to date, then see what is happening with your hard drive it should not be loosing space, if it’s still loosing space then you probably have an operating system problem more likely than an ST3 problem, as no one else is experiencing this I assume as Peter would immediately know.
Cheers Damir