If IMAP cache is enabled then the command to directly delete message in Junk folder ("Empty") is greyed out even if the option is enabled in preferences. Is this a bug? If it is intended then the option in server settings shouldn't be shown.
Works for me or I don't understand your problem.
Please look at attached screenshots. There are no plugins enabled. It is a default Roundcube 1.0 stable.
Screenshot 1 (wo_cache.png): 'imap_cache' and 'messages_cache' is disabled => "Empty" command is enabled
Screenshot 2 (w_cache.png): 'imap_cache' and 'messages_cache' is enabled => "Empty" command is greyed out (disabled)
In bove screenshots "Junk" mailbox is selected and option to directly delete messages in Junk folder is enabled (Settings -> Server Settings).