Hi, I also was hit by this bug; I wouldn't rate it minor: It is very annoying, and contrary to all documentation, including the man page.
Since the ~/.fluxbox files seem to be autogenerated upon first use from the template in /etc, it should really be easy to just change the default in ~/.fluxbox/init. Otherwise, the issue should be documented. Regards, Frank -- Frank Küster Inst. f. Biochemie der Univ. Zürich Debian Developer