Apply all the fixes from: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ 2.
Update cygwin Problems can arise from using older versions of cygwin, or selective ("pick and choose") installations of cygwin.
Be sure that you install everything in places without empty spaces (avoid "C:\Program Files\").
But by default cygwin uses your windows login (something like "First Name Last Name") to create the /home/user_folder.
Only the minimal base packages from the Cygwin distribution are installed by default.This is one of the fundamental problems Cygwin attempts to solve.Linux programs expect that when spawning a new process, the new process will have the same memory layout as the old one but Windows actively changes the memory layout whenever a new process is started.Notes from the EMBOSS developers: We recommend doing a full cygwin installation or problems may arise with creating the DLLs.2) cygwin (and EMBOSS, and other linux/unix programs) don't like empty spaces in names.