I have tested that and it seems to work both way here (Debian testing + Jnotify 0.94 + openjdk6).
give it a try using openjdk6 instead of 7. The desktop sync is bound to a sun JRE6 on windows.
However, Sync works only when using CLI file management. upstream sync of files created through the gnome UI fails quite quickly.
For example, GNOME file manager (like most UI tools I guess) uses a default name when creating a new folder, then rename it. The DesktopSync client does not deal with this properly on Linux and still serach for pathes with the old name…
Linux not being supported, I guess there is nothing to expect about this at the moment.