While on the commandline, you can enter multiple roots to be backed up, like: obnam --config=/etc/obnam.cnf backup sftp://user@host/etc sftp://user@host/home
The same is not possible when setting the root in a configfile. Setting multiple root= entries simply overrides the previous ones and only picks up the last one; setting them all on one line, space-delimited, like on commandline gets interpreted as one large filename with spaces.
This turns out to be a problem in the config file: you need to set all the roots in one root= line, instead of having one root= per root.
[config]
root = /home/you, /home/them
That'll work. I've added something to the manual page to explain that better. Sorry about the confusion. --liw