I've had this very problem and upgrading my Cygwin didn't make the trick.

I finally isolated the problem on the script which launched rsync, this script had those lines:

REM Set HOME variable to your windows home directory. That makes sure REM that ssh command creates known_hosts in a directory you have access. SET HOME=%HOMEDRIVE%%HOMEPATH%

It seems that under Windows Scheduler the HOMEDRIVE and HOMEPATH aren't initialized so HOME was not set and ssh.exe hung while asking to accept the remote key.

After initializing HOME to a known directory it started working fine.

I've had this very problem and upgrading my Cygwin didn't do the trick.

I finally isolated the problem to the script which launched rsync; the script had these lines:

REM Set HOME variable to your windows home directory. That makes sure 
REM that ssh command creates known_hosts in a directory you have access.
SET HOME=%HOMEDRIVE%%HOMEPATH%

It seems that under Windows Scheduler the HOMEDRIVE and HOMEPATH aren't initialized so HOME was not set and ssh.exe hung while asking to accept the remote key.

After initializing HOME to a known directory it started working fine.