I opened up a pull request for this issue a few weeks ago:
https://github.com/vim/vim/pull/505

The short version is that relative paths are handled differently in Cygwin
compared to other platforms. The most obvious manifestation of the bug is that
`fnamemodify('.', ':.')` returns an empty string instead of '.'. This breaks
some plugins (e.g. Unite's grep uses a sensible default path of '.' but that's
broken in Cygwin). The fix (in the pull request and copied below) is to use the
CCP_RELATIVE flag when requesting a full path name from any type of path name.

Thanks,
Jacob Niehus

--------------------------------------------------------------------------------

diff --git a/src/os_unix.c b/src/os_unix.c
index 314a906..7b98f9c 100644
--- a/src/os_unix.c
+++ b/src/os_unix.c
@@ -2500,7 +2500,8 @@ mch_FullName(fname, buf, len, force)
      * This helps for when "/etc/hosts" is a symlink to "c:/something/hosts".
      */
 # if CYGWIN_VERSION_DLL_MAJOR >= 1007
-    cygwin_conv_path(CCP_WIN_A_TO_POSIX, fname, posix_fname, MAXPATHL);
+    cygwin_conv_path(CCP_WIN_A_TO_POSIX | CCP_RELATIVE,
+           fname, posix_fname, MAXPATHL);
 # else
     cygwin_conv_to_posix_path(fname, posix_fname);
 # endif

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