This is a known bug. The only workaround I've found is to create a new file and copy the content from the old one page by page and paste in place in the new file.
Thanks for the quick response. I only wanted to print as booklet for proofing purposes. Does the issue ever cause issues when going to a digital press? I haven't had any trouble with other jobs I've sent, so I don't want to risk anything going wonky if I copy and paste into a new doc.
I've only seen it in association with Print Booklet, which requires that all pages be the same size. I don't think there will be any problem in sending to print, especially if you provide an exported PDF. You could probably do your proof by using Acrobat's booklet function, and it would be more releable since it uses the same file you send to the printer.