After the Restore
 

I did a restore from an SD backup and it worked but I found that some settings didn't come with the restore. The restore was to a new machine.

The screen saver was the default instead of the one I had selected. When I opened iPhoto, it prompted for whether or not I wanted to use a camera with the program. When I opened Numbers and iTunes it prompted similar questions.

Shouldn't a restore bring all that over?

As far as I can tell, my data is there.

Some preferences are stored "by host" -- that is, they don't restore when the Mac changes (even though the files are there).