There are a couple of bugs hopefully to be fixed in the next release of 11.2. However, in some cases it all depends on the name of the bookmark, meaning that under some circumstances, BM01 is not the same as User\BM01 or Document\BM01
If you have already tried to rename your bookmarks, I'd bet on the bug. If you have not already, log a Support ticket with as much information as possible and if possible, a sample document with an step by step. As a customer, you can use the new Qoncierge service who will help you on the process with Support.
I happen to recall a bug fixed in v10 SR6 according to the Release Notes document, and something similar in the Update 1 of v11 SR1.
Let us know in any case.
Hope that helps,