JMarc, Are you interested in making the 1.4.3 source package compatible with cygwin? I have been on the cygwin-package list for a while and it seems that maintaining a cygwin package is not terribly difficult or time consuming. Since 1.4.3 compiles and works well under cygwin, it might be a good idea to submit lyx as a standard cygwin application.
I have not read http://cygwin.com/setup.html in detail, it seems to me that we only need a few additional description files, and adding scons-local to the source package. Bo