The basic problem is that sometimes when I do
git pull upstream master
I get
remote: Counting objects: 172, done. remote: Comp
This is addressed here: http://cygwin.wikia.com/wiki/Rebaseall
In short, close all windows and run this:
C:\cygwin\bin\dash.exe -c '/usr/bin/rebaseall -v'
This fixes all related issues with forking. I had issues with forking aspell from emacs as well as git.