In Auto mode, if you have the Suffix Mapping table entry for '.bin' (the correct ending for MacBinary files) set to MacBinary, then Yummy will auto-decode the file on download, resulting in the original file, but with file name length limitations. This can lead to truncated file names.
I just checked my own Suffix Mapping table in the default settings and no auto-decoding is done because '.bin' files are marked to transfer in Binary (no encoding at all, raw data, as is).
In v1.9.3 the Suffix Mapping table is available via a button in the Obscure panel of the Preferences. In earlier versions it's in the menu bar off the Transfer menu.
If you're still getting problems, it's probably best to contact me in support (support @ yummy software dot com) and send me an FTP Transcript file of a problem download.