First I have heard of such a problem. My initial suggestion would be that the Keychain entry is incorrect / doesn't match the host, or is inaccessible by Yummy FTP, so please check that. Other than that, I suggest to send screenshots of your Bookmark editor window (both tabs, please) to the support email address for me to check, or alternatively send me your Bookmark file. I'll also need to have the exact text of the 'Where' field in the Info window for the Keychain entry in the Keychain Access application. This way, I'll be able to tell you what is happening.
Thanks,
Jason