Output directory names

I'm running an experiment with bob.bio.vein and, surprinsingly the output directories do not get their "database" and "protocol" settings correctly replaced. I get:

$ ls ~/user/database-name/sub-directory/
rlt/

My settings for the sub-directory seem correct. The database-name and sub-directory I think should correspond to the database name and the protocol name. The protocol string is correctly set on my option files. I don't understand why these strings are not being correctly replaced. Very likely, because of our patch in #26 (closed). A fix is required.