To reproduce:

1. Install Ocaml on Windows 10 via https://fdopen.github.io/opam-repository-mingw/. I'm using version 4.04.0+mingw64.

2. Install merlin via opam. I am currently pinned to 8ea5c48, but also saw this issue on 2.5.5.

3. Install Emacs via https://sourceforge.net/projects/emacsbinw64/. (I didn't test with other builds.) Version: GNU Emacs 25.1.1 (x86_64-w64-mingw32) of 2016-09-21

4. Add merlin to .emacs by copying the code at https://github.com/ocaml/merlin/wiki/emacs-from-scratch#installing-merlin-and-its-emacs-mode-with-opam.

5. Open Emacs via ocaml-env-win.

6. Open an Ocaml buffer and save. A cmd window will open very briefly any time merlin is invoked.

In contrast, ocp-indent works without a hitch, so this seems to be a problem with Merlin specifically.

The actual checking behavior works as expected, which is great. The cmd window a) is a visual annoyance and b) captures keystrokes, since it pops up during completion.