Not too sure if this helps or is the reason, but there are 2 types of bookmarks, document and user bookmarks.
If you have created the bookmark as a document bookmark (tick box in add bookmark options) when you were in the app with a developer account, then an end user cannot remove this bookmark. An end user can only remove their own custom created bookmark.
Can it be as simple as this or do you think this might be a bug. I'm testing it in my enviro now and will tell you the results.