2012-05-02 cgf-000001 This fix was due to a bug report on the Cygwin mailing list: http://cygwin.com/ml/cygwin/2012-05/msg00009.html strace showed that ssh-agent was checking the parent pid and getting a 1 when it shouldn't have. Other stuff looked ok so I chose to consider this a smoking gun. Going back to the version that the OP said did not have the problem, I worked forward until I found where the problem first occurred - somewhere around 2012-03-19. And, indeed, the getppid call returned the correct value in the working version. That means that this stopped working when I redid the way the process pipe was inherited around this time period. It isn't clear why (and I suspect I may have to debug this further at some poit) this hasn't always been a problem but I made the obvious fix. We shouldn't have been setting ppid = 1 when we're about to pass off to an execed process. As I was writing this, I realized that it was necessary to add some additional checks. Just checking for "have_execed" isn't enough. If we've execed a non-cygwin process then it won't know how to deal with any inherited children. So, always set ppid = 1 if we've execed a non-cygwin process.