Could not duplicate problem on my computer.
My computer uses a non standard MSys2 installation; but, that just results in a different path displayed.
My MSys2 installation used is installed in "C:\building\msys64" instead of normal "C:\msys64".
I am guessing a bad compiler toolchain setting is the cause.
-------------- Clean: Release in gtk_manual_setup (compiler: GNU GCC Compiler)---------------
Cleaned "gtk_manual_setup - Release"
-------------- Build: Release in gtk_manual_setup (compiler: GNU GCC Compiler)---------------
x86_64-w64-mingw32-gcc.exe -Wall -IC:/building/msys64/mingw64/bin/../include/gtk-3.0 -IC:/building/msys64/mingw64/bin/../include/pango-1.0 -IC:/building/msys64/mingw64/bin/../include -IC:/building/msys64/mingw64/bin/../include/glib-2.0 -IC:/building/msys64/mingw64/bin/../lib/glib-2.0/include -IC:/building/msys64/mingw64/bin/../include/harfbuzz -IC:/building/msys64/mingw64/bin/../include/freetype2 -IC:/building/msys64/mingw64/bin/../include/libpng16 -mms-bitfields -IC:/building/msys64/mingw64/bin/../include/fribidi -IC:/building/msys64/mingw64/bin/../include/cairo -IC:/building/msys64/mingw64/bin/../include/lzo -IC:/building/msys64/mingw64/bin/../include/pixman-1 -mms-bitfields -mms-bitfields -mms-bitfields -mms-bitfields -mms-bitfields -mms-bitfields -mms-bitfields -IC:/building/msys64/mingw64/bin/../include/gdk-pixbuf-2.0 -mms-bitfields -mms-bitfields -mms-bitfields -IC:/building/msys64/mingw64/bin/../include/atk-1.0 -mms-bitfields -mms-bitfields -mms-bitfields -pthread -mms-bitfields -O2 -c C:/Users/stahta01/Documents/test/gtk_manual_setup/main.c -o obj/Release/main.o
C:/Users/stahta01/Documents/test/gtk_manual_setup/main.c: In function 'main':
C:/Users/stahta01/Documents/test/gtk_manual_setup/main.c:34:3: warning: 'gtk_vbox_new' is deprecated: Use 'gtk_box_new' instead [-Wdeprecated-declarations]
34 | vbox = gtk_vbox_new (TRUE, 6);
| ^~~~
In file included from C:/building/msys64/mingw64/include/gtk-3.0/gtk/gtk.h:286,
from C:/Users/stahta01/Documents/test/gtk_manual_setup/main.c:2:
C:/building/msys64/mingw64/include/gtk-3.0/gtk/deprecated/gtkvbox.h:61:13: note: declared here
61 | GtkWidget * gtk_vbox_new (gboolean homogeneous,
| ^~~~~~~~~~~~
C:/Users/stahta01/Documents/test/gtk_manual_setup/main.c:37:3: warning: 'gtk_button_new_from_stock' is deprecated: Use 'gtk_button_new_with_label' instead [-Wdeprecated-declarations]
37 | button = gtk_button_new_from_stock (GTK_STOCK_DIALOG_INFO);
| ^~~~~~
In file included from C:/building/msys64/mingw64/include/gtk-3.0/gtk/gtk.h:54,
from C:/Users/stahta01/Documents/test/gtk_manual_setup/main.c:2:
C:/building/msys64/mingw64/include/gtk-3.0/gtk/gtkbutton.h:103:16: note: declared here
103 | GtkWidget* gtk_button_new_from_stock (const gchar *stock_id);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
C:/Users/stahta01/Documents/test/gtk_manual_setup/main.c:37:3: warning: 'GtkStock' is deprecated [-Wdeprecated-declarations]
37 | button = gtk_button_new_from_stock (GTK_STOCK_DIALOG_INFO);
| ^~~~~~
C:/Users/stahta01/Documents/test/gtk_manual_setup/main.c:41:3: warning: 'gtk_button_new_from_stock' is deprecated: Use 'gtk_button_new_with_label' instead [-Wdeprecated-declarations]
41 | button = gtk_button_new_from_stock (GTK_STOCK_CLOSE);
| ^~~~~~
In file included from C:/building/msys64/mingw64/include/gtk-3.0/gtk/gtk.h:54,
from C:/Users/stahta01/Documents/test/gtk_manual_setup/main.c:2:
C:/building/msys64/mingw64/include/gtk-3.0/gtk/gtkbutton.h:103:16: note: declared here
103 | GtkWidget* gtk_button_new_from_stock (const gchar *stock_id);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
C:/Users/stahta01/Documents/test/gtk_manual_setup/main.c:41:3: warning: 'GtkStock' is deprecated [-Wdeprecated-declarations]
41 | button = gtk_button_new_from_stock (GTK_STOCK_CLOSE);
| ^~~~~~
x86_64-w64-mingw32-gcc.exe -o bin/Release/gtk_manual_setup.exe obj/Release/main.o -LC:/building/msys64/mingw64/bin/../lib -lgtk-3 -lgdk-3 -lz -lgdi32 -limm32 -lshell32 -lole32 -Wl,-luuid -lwinmm -ldwmapi -lsetupapi -lcfgmgr32 -lpangowin32-1.0 -lpangocairo-1.0 -lpango-1.0 -lharfbuzz -latk-1.0 -lcairo-gobject -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lgobject-2.0 -lglib-2.0 -lintl -s
Output file is bin\Release\gtk_manual_setup.exe with size 19.00 KB
Process terminated with status 0 (0 minute(s), 1 second(s))
0 error(s), 5 warning(s) (0 minute(s), 1 second(s))