Note: this is related to https://java.net/jira/browse/JAXB-965 but IS not identical. See below.
It is different in two respects: (1) it showcases the same kind of bug but in an absolutely minimal setting (with only three, extra-short, xsd files) (2) it demonstrates that in this particular setting, the Ant xjc task fails but the command-line invocation of xjc succeeds which is unsettling but may provide a hint as to the location of this bug.
Here we have three minimal xsd files where invoking the Ant xjc tasks with episodic compilation fails with "unable to honor this schemaBinding" whereas invoking the xjc tool from the command line succeeds. You can view the failure with:
git clone https://github.com/mperdikeas/unable_to_honor-narrowdown.git && cd unable_to_honor-narrowdown && ant
whereas the invocation of the invoke-xjc-2.2.7 succeeds.