Can you explain what you are doing? Is D:\The Bat! a new, empty folder? Or mayb a new folder that you copied the contents of a previous mail folder to..?
I'm not sure what sort of processing is supposed to be going on there. If The Bat is fetching a huge amount of mail or indexing a very large message base, those things can take time. But I'm not sure if any such thing is supposed to happen when you're in the Preferences dialog.
Does the LED activity light of your harddrive(s) blink, showing that it's busy reading/writing?
I volunteer as a moderator to help keep the forum tidy. I do not work for Ritlabs SRL.