After upgrading doxygen to the current 1.7.1 no warnings were found. Some investigation revealed that somewhere on the way from 1.5.1 to 1.7.1 the output changed slightly and "Warning"became "warning".
After modifying the redirected output with
perl -i.bak -pe 's#: Warning: #: warning: #' builds/doxygen-report/doxygen-stderr.txt
everything seems to work fine again.
So I suspect there is some regex in the doxygen plugin that needs changing