No idea about your specific issue but I use a simple batch file to do my backups. I use robocopy (you'll have to download robocopy) for primary backups to one drive and xcopy for cumulative backups to another. Both drives are internal. If you do want to go down this route and are using USB drives you will have to ensure they are allocated the same drive letter each time you plug them in.
Windows Backup has never been a very reliable backup tool in my opinion and I've never bothered to use it for that reason. I usually just script out my home backups or use a paid tools in my job experiences.
There are a number of freely available tools for backup purposes but I can't speak to them at all.