The current version of Cygwin has a bug which causes update_cygwin.cmd to fail. When ssh-keygen.exe is run from a normal non-Cygwin command prompt, the following occurs:
C:\cygwin\home\root\VCL\Scripts>C:\Cygwin\bin\ssh-keygen.exe -t rsa1 -f C:\cygwin\etc\ssh_host_key -N ""
Generating public/private rsa1 key pair.
8 [main] ssh-keygen 224 exception::handle: Exception: STATUS_ACCESS_VIOLATION
2114 [main] ssh-keygen 224 open_stackdumpfile: Dumping stack trace to ssh-keygen.exe.stackdump
61325 [main] ssh-keygen 224 exception::handle: Exception: STATUS_ACCESS_VIOLATION
68272 [main] ssh-keygen 224 exception::handle: Error while dumping state (probably corrupted stack)
Running rebaseall doesn't help. The command succeeds if run from a Cygwin shell.