Yes, and I can also test it with my home grown qt3. Why don't you try to build qt3 following http://wiki.lyx.org/LyX/LyXOnCygwin ?
I was afraid of the potential configuration/link differences between cygwin/qt3 and standalone qt3.
Then, what you do with this qt3 you simply redo it with the cygwin qt3. So, no need to downgrade cygwin.
I understand, downgrading has been painful. If I can eventually do that, at least I can test your autoconf patches using the native build. Bo