Huh! I've never seen that... Do you know what version of the autotools is bundled with your mingw/Msys2 setup?
This is an "it has always worked for me" sort of answer, but I think I have a pretty old version of the autotools in my tarball that I use for setting up new machines, so it may be immune.
FWIW, and this might be worth a shot too, I don't do the "NOCONFIGURE=1 ./autogen.sh" approach at all generally - rather, I just type "make" in the top of the clean checkout. The fltk Makefile then detects that autoconf et al have not run, sets up the defaults and the missing config bits, and runs the configure (with default values) and builds OK.
If I want non-default configure options, I break in at this point and re-run "./configure" manually with the needed settings...
So far, this Just Works... Here's a grab of what that looks like, from a clean sheet...
/d/Support
$ git clone https://github.com/fltk/fltk.git fl_test
Cloning into 'fl_test'...
remote: Enumerating objects: 75607, done.
remote: Counting objects: 100% (1624/1624), done.
remote: Compressing objects: 100% (854/854), done.
remote: Total 75607 (delta 969), reused 1260 (delta 762), pack-reused 73983
Receiving objects: 100% (75607/75607), 28.24 MiB | 2.75 MiB/s, done.
Resolving deltas: 100% (61795/61795), done.
Updating files: 100% (1333/1333), done.
/d/Support
$ cd fl_test
/d/Support/fl_test (master)
$ make
Makefile:17: makeinclude: No such file or directory
autoconf
if test -f config.status; then \
./config.status --recheck; \
./config.status; \
else \
./configure; \
fi
checking build system type... x86_64-pc-mingw64
checking host system type... x86_64-pc-mingw64
checking for gcc... gcc
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for pkg-config... no
checking for wtypes.h... yes
checking for gdiplus.h... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for nroff... no
checking for groff... no
checking for doxygen... /d/Tools/doxygen/bin/doxygen
checking for ranlib... ranlib