[author updated this post]
There is a know issue with ckeditor and boxes that seems to be specific to open atrium--at least it the same problem has now been reported by a couple of users. See: http://drupal.org/node/1448940 -- the patch provided does not solve the problem with boxes in Open Atrium.
I was attempting to install the latest CKeditor in a new installation of OA. All seems to be working nicely. Thanks in part to http://linuxhelp4me.com/documentation/node/52 -- having set the CKeditor to use its own CSS rather than the inherent from the OA theme.
I can create content and add a bullet list using CKeditor on a node which is full html. When I save it and search for the node in the database, the tags are there. -- however, on my first test I was editing a box on the dashboard. It turns out this was not a fair test. The CKeditor work great on new nodes. It just does not play nice with boxes under OA.
The input formats are saved to include the UL and LI tags--but I would have thought that the html filtering would strip the tags as the data is saved to the database rather then as the saved data is read back and served. The problem is that the UL LI tags will not render when I revisit the node. I see them in the database so I can only assume that the sites CSS is stripping them out after it reads the saved node from the database.
Any suggestions for applying full or filtered html to contents in boxes in OA?