I think I found the culprit. In build\src\cmake_install.cmake there is a (hardcoded?) reference to the 1.3.28 version.
Let me check what happens if I just clear my build folder and try again.
Edit: nope, the version stays 1.3.28 even though 1.3.29 seems to be installed.
Edit 2: this value seems to come directly from darktable\cmake\windows-macros.cmake. But apparently no longer reflects the current up to date version of GraphicsMagick. Seems a bit tricky to hardcode versions in your makefile, or am I missing something? @houz?