The FTP encoding issue has been addressed in the current nightly builds: you can now choose which encoding to use in the FTP panel of the 'Connect to server' dialog (UTF-8 by default).
The FTP encoding is saved with your credentials, which allows muCommander to 'remember' which FTP encoding to use for a particular server. If you choose to save the credentials to disk, the encoding value will be saved and reused next time muCommander is started.
There is however one limitation: you cannot change the encoding of a particular FTP connection 'on the fly'. To change it, you'll need to disconnect any active FTP connection to the server (you can do so in the 'Show active connections' dialog), and then reconnect to the server with the new encoding. This requires more effort than strictly necessary if you need to do some 'trial and error' in order to figure out which encoding an FTP server is using. We might implement a better way to do this in the future...
But in your case, since you seem to know which encoding to use, it should be as easy as 123 :)
I hope that will fix your problem, please us know if it did !