I have a reproducable error that I just discovered. I run Cygwin on a Win2000 system and connect to my FreeBSD 5.1 system at home over SSH v2 tunnelling. I run X apps remotely using Xwin -multiwindow. For the most part, things have worked great.
I just tried running gftp (2.0.14 installed from the FreeBSD ports system) and found that as soon as I try to initiate a transfer, Xwin will crash on my local system. I realize this is a bit obscure, so if no one else has experienced this I understand, but can I do anything to help you track down the cause?