If you're on Windows and using RC5, download an updated executable if you haven't already. This is the most recent: http://filesmelt.com/dl/zelda-w6.zip
The biggest issues remaining are that ZC sometimes hangs on exit and that save files are sometimes wiped for no apparent reason. I think I might finally have gotten those fixed, but both problems occur sporadically, so I can't be certain. If you're using an updated RC5 executable and encounter either of those problems, let me know right away.
