I am also having problems with the Captivate 5.5 PDFs. The animations don't play (these are AS3 from the Cap 5.5 Gallery), and the navigation buttons don't appear unless I first select a page from the TOC.
I was not able to reproduce the issue at my end. Can you please create a new captivate project and export it to PDF and then check that file.
There is no issue as such with Captivate generated PDF opening in the reader version 9 and above. Can you please email me and I can check from my end. My mail is firstname.lastname@example.org
I do have exactly the same problem with acrobat XI and captivate 6 !!
Also having this issue following an automatic update from Reader 10.1.4 to.10.1.5 for PDFs generated in Captivate 5.5 which have had no problems for over a year, now suddenly after this update they don't work. Seeing plenty of posts regarding the problem but no resolutions as yet; if I find anything I'll post here.