I think that the newer (SL5600) usb drivers for the Zaurus on Windows work differently. This is what causes the incompatibility with the newer version of Qtopia Desktop 1.7. I believe the new drivers sync with out using tcp/ip. I currently have the Sharp Rom installed and the Sharp version of the desktop (win) which sync fine. I see no usb network devices and I am also unable to ping my Zaurus. Perhaps using an older Zaurus network driver would work. OZ syncs nicely with the Qtopia Desktop 1.7 on linux, but I don’t know how to connect it to the network via a windows box. Do you have a dedicated Linux box you could use as a router to your Zaurus? You might also try Qtopia 1.7 (win) and setting your IR as a network device (I have no idea if this will work).
btw, filezilla is an excellent ftp/sftp client
http://sourceforge.net/projects/filezilla/