I first noticed this running a locally-installed cygwin netcat listener (latest and greatest) on my laptop and then running IR\IRCR-NC.bat script on Helix. A simple way to reproduce this is to start a cygwin bash shell and then run one of the tools from IR\Cygwin on the Helix CD. You should see errors like this:
9 [main] ? (6104) e:\IR\Cygwin\nc.exe: *** fatal error - system shared memory version mismatch detected - 0x8A88009C/0x2D1E009C.
This problem is probably due to using incompatible versions of the cygwin DLL.
Search for cygwin1.dll using the Windows Start->Find/Search facility
and delete all but the most recent version. The most recent version *should*
reside in x:\cygwin\bin, where 'x' is the drive on which you have
installed the cygwin distribution. Rebooting is also suggested if you
are unable to find another cygwin DLL.
Pretty self explanatory.
Jimbob