Pieces of the contents of configure.ac, Makefile.am, and related files are included in the build output of GNU Autotools when the source archives for Guacamole are generated, including the ASF boilerplate comment. Because autotools also inserts its own FSF boilerplate at the top of these generated files, we end up with a confusing combination of FSF and ASF headers.
This concern was brought up during the release VOTE for 0.9.12-incubating, and discussed in
LEGAL-300. The final conclusion of this was:
... I would suggest simply to edit the license header in Makefile.am such that it is correct both in situ (in Makefile.am) and when transcluded into Makefile.in. Basically, add a sentence or two explaining the licenses of Makefile.am and Makefile.in and that verbatim transclusion is occuring.
The above change should be made wherever necessary, once suitable wording has been determined.