I ran a backup where I selected specific files on the machine (one of the files was c:\program files\amd\ccc2\install\ccc2_install.exe - an installer for a video driver progaram). When the backup was run, the file was not backed up and there was no indication in the log file why it wasn't.
As it turns out, the file was deteremined to be part of the "system state" and was only included when I backed up the system state. (and could not be restored unless I restored the entire system state).
This is very concerning since there doesn't seem to be a way of predicting what files are system state and what files are not. (most of the files in the ccc2 subtree *were* backed up outside the system state, only one of them was considered to be "system state").