Today I had a problem where my FTP client of choice, Panic Software's Transmit, where I changed the server software and any time thereafter SSH connections gave a "Permission Denied" error. As it turned out the problem wasn't permissions but rather the server's SSH identity changed and Transmit was getting confused. A little looking around didn't turn up anything obvious - there was no preferences option to force it to re-validate the identity, it just kept failing. So on the off-chance I took a look at the file ~/.ssh/known_hosts and sure enough there was an entry for the server - I removed the server's line, re-connected and it worked again! Now to submit a feature request...