Could this be related? It just started happening now.
$ make -C lisp custom-deps
make: Entering directory '/d/Devel/emacs/repo/trunk/lisp'
make[1]: Entering directory '/d/Devel/emacs/repo/trunk/lisp'
GEN cus-load.el
INFO Scanning files for custom...
INFO Scanning files for custom...10%
INFO Scanning files for custom...20%
INFO Scanning files for custom...30%
INFO Scanning files for custom...40%
INFO Scanning files for custom...50%
INFO Scanning files for custom...60%
INFO Scanning files for custom...70%
INFO Scanning files for custom...80%
INFO Scanning files for custom...90%
INFO Scanning files for custom...100%
INFO Scanning files for custom...done
INFO Generating ./cus-load.el...
Version must be a string
make[1]: *** [Makefile:152: cus-load.el] Error 127
make[1]: Leaving directory '/d/Devel/emacs/repo/trunk/lisp'
make: *** [Makefile:150: custom-deps] Error 2
make: Leaving directory '/d/Devel/emacs/repo/trunk/lisp'