> By contrast, compilation of CEDET was probably run somewhere on drive
> D:, so /home/epich/sw/cedet/lisp/cedet/loaddefs.el got D: prepended to
> it.

No, it wasn't.  I type these two commands at the Cygwin shell without
changing anything, including pwd:

emacs -batch --no-site-file --eval '(setq debug-on-error t)' -l
"../../cedet-remove-builtin.el" -L . --eval '(progn (require (quote
cedet-compat)) (require (quote mode-local)))' -L ../eieio/ -L ./ -L ./
--eval '(progn  (setq generated-autoload-file
"/home/epich/sw/cedet/lisp/cedet/loaddefs.el"))' -f batch-update-autoloads
/home/epich/sw/cedet/lisp/cedet

emacs -batch --no-site-file --eval '(setq debug-on-error t)' -l
"../../cedet-remove-builtin.el" -L . --eval '(progn (require (quote
cedet-compat)) (require (quote mode-local)))' -L ../eieio/ -L ./ -L ./
--eval '(progn  (setq generated-autoload-file
"/home/epich/sw/cedet/lisp/cedet/loaddefs.el") (message "DEBUG: expanded
file name is %s" (expand-file-name "/home/epich/sw/cedet/lisp/cedet")))'
/home/epich/sw/cedet/lisp/cedet

The first yields an incorrect "d:" prefix, the second the "c:" prefix.  Why
would this be?  This is evidence of an Emacs bug.

> I don't know why you invoke Emacs from the Cygwin Bash.  I suggest not
> to, or to switch to a Cygwin build of Emacs.  Mixing these two
> environments is asking for trouble.

When I set up Cygwin, I did not install Cygwin's Emacs installation.  There
is no conflict with an alternate Emacs.  I am merely using Cygwin's GNU
Make to execute makefiles, which correctly invoke the Windows emacs.exe
binary.  Why shouldn't that work?