We're currently trialing a new folder screen on the beta server. To try it out, just login at http://www.fastmail.fm/beta/, and click on the (Edit/Refresh) link at the top of the folder list on the left hand side of the mailbox screen.
The new folder screen is designed to solve a number of issues.
In an effort to allow more options on folders in the future as well (eg. we'd like to add the ability to set folders to auto-delete messages older than a certain time), we've moved the setting of options on folders to a separate screen, rather than having one big grid. When setting the options on multiple folders, we've tried to follow the iTunes approach which uses checkboxes to control exactly options you want to set.
For more details and feedback, please check out this forum thread