I realize there are a few other questions about why Cygwin is apparently slow, but this case seems to be unique.
I had some issues where things were reporting lots of er
I had a similar problem, fixed by removing disconnected network shares.
http://cygwin.com/faq/faq-nochunks.html#faq.using.slow http://cygwin.com/ml/cygwin/2010-06/msg00510.html (read all replies)
You can look into this as well:
http://cygwin.com/acronyms/#BLODA
gl