Incomplete config.properties file in built assemblies

Over at the Opencast project (https://github.com/opencast/opencast) we rarely (1/20 or so) have assemblies seem to build correctly, but a number of libraries required for the assembly to boot with all installed modules will be missing from config.properties.  A repackage of the same codebase and built artifacts resolves the issue, so this seems to be related to the assembly itself rather than the underlying modules.  This also seems to be independent of our branches, and versions - we've been observing this off-and-on for more than a year but I've just never gotten around to filing this.

Things attached:

• working and broken.log: full build outputs (including component compilation) of the working and failing builds, respectively
• working and broken.properties: the config.properties generated in the working, and failing builds, respectively.