File manifest implementation still doesn't work reliably using ZipArchive

Automatic backups still don't work reliably on my personal site, which is hosted on WebFaction. The plugin defaults to using ZipArchive as the backup process.

What I suspect is happening, but haven't proven, is that the plugin reports that the backup process has been killed when it hasn't. The application then spawns a new backup process which clobbers the other backup process and the whole house falls down.