I've been backing up using the "clone" rather than the backup option to ensure that I had copies of all my system files. I noticed that some of my data had not been copied on my most recent back-up. Here's what Intego said when I asked Tech Support:

"The Clone operation will not be able to determine if files have changed,
only if they are present. It does not provide the type of modification
checking for an incremental backup the way that the backup script does.

If you are going to Clone as a weekly backup method we suggest that you
first erase the destination disk and then clone so that all of the current
modifications of the files are copied.

We are hoping to address this in an upcoming release of the product so that
the Clone operation will abide by the same incremental rules as the Backup
script does. We apologize for the frustration and confusion his has caused."

Which means that the 'cloned" back-ups I've been making for the last two months are useless. Thanks, Intego.

I'm not sure that what Intego says is even true, since the files that Personal Backup failed to copy were new, not changed, and it certainly should have noticed them. Mind you they contained Microsoft software, so you can't blame it for being a bit reluctant.