The recent update broke some code in the Flex Page course format. Users are unable to add, delete or edit files in their Course Documents pages in courses formatted as Flex Page layouts.
Moodlerooms has been able to identify the error and is now testing a patch to repair it. They should be able to apply the patch sometime early next week (the week of Jan. 6.) We will keep you posted here in the Site News section.
If you don't want to wait for the patch, you can reformat your course in one of the single-page layouts that appear to be more compatible with Moodle 2.x versions. Email us at firstname.lastname@example.org if you want to find out more about that option.