I am also having a similar problem. I usually ignored the "update is available" prompt, even though it caused the emulator to freeze up several times, but just a few minutes ago I downloaded it and now the game I was playing will not load at all. I don't think the ROM is in any kind of zipped archive.
EDIT: I cannot believe this. I just retried it and my twenty-hour save file of Fire Emblem 3 is completely gone because I upgraded. The emulator does not seem to recognize the translation patch I have in the folder with the ROM - the game is loaded in Japanese. The other save file I had for a different game has been erased. What happened, and what was the point of updating?
I guess I should explain the sequence of events, so it is clear what happened.
I was playing earlier this morning. I tried to reset Fire Emblem: Mystery of the Emblem (running with a translation patch - the ROM was not hard-patched, but the ips was in the same folder as the ROMs), and as I went to the home menu, the update prompt appeared and caused the emulator to freeze up (which seems to be a common occurrence ever since I started getting that prompt about a week ago).
I turned the Wii on and off, went back to the menu, and finally answered "yes" to the update prompt because I was tired of it freezing the emulator. It seemed to update without any problems (the only noticeable difference was that the font changed), but Fire Emblem did not run. The first two times I tried to run it, it went to a black screen with code on it and reloaded to the Homebrew Browser in eight seconds (or it may have been the SNES9xGX menu, I'm not sure now). The third time, it went to a black screen and made a loud buzzing sound. I turned off the Wii.
An hour or so later, I came back and turned it back on. When I went to the emulator's menu, it gave me a prompt to update again, strangely enough. I accepted, and it seemed to update normally again. But when I tried to load either of my two SNES ROMs, they were fresh - there were no save files detected. The Fire Emblem ROM ran without the patch's effects (so it had no save files and was in Japanese). There were save files in the saves folder, but when I put the SD card into my PC and looked at the times they were last modified, it seems like the files were just created when I started the ROMs back up.
Edited 2 time(s). Last edit at 04/10/2010 02:52AM by Hylian7.