This entry is actually directed to the developer.
I was able to select two directories for a differential backup as follows:
Locations=|C:\\Documents and Settings\\HP_Owner\\My Documents\\CherFore\\Resume|C:\\Documents and Settings\\HP_Owner\\My Documents\\CherFore\\Scripts
The first run created a base file with the Resume directory, and a timestamped file with the Scripts directory.
When I updated files in both directories and ran the differential backup again, only the update in the Resume directory was done successfully. The attempt to pick up the change in the Scripts directory resulted in the following error messages:
Creating file list, this may take some time.
7-Zip 4.65 Copyright (c) 1999-2009 Igor Pavlov 2009-02-03
File already exists
This can be bypassed by setting up jobs for each directory, but I don't think you are supposed to have to do that.