Happened when building Gpg4win on a system with fltk-dev installed:
configure:10958: checking for fltk-config configure:10976: found /usr/bin/fltk-config configure:10989: result: /usr/bin/fltk-config configure:11005: checking for FLTK 1.3 configure:11015: result: yes
This then resulted in build errors.
Low prio as this affects only cross compiling and the fix is obviously to disable fltk.