Thank you for your post.
I am unable to replicate the problem. I installed FileMaker Pro 12.0v4 on a MacBook running Mac OS X 10.6.8. I created a database file with one Container field, sized the Container field to be almost a page in height, and set the Container field for interactive content. I inserted the FileMaker Acknowledgements PDF into the container field, and everything appears fine. Below is the screen shot along with the About This Mac and About FileMaker Pro windows.
I then quit FileMaker Pro 12.0v4, and updated to FileMaker Pro 12.0v5.
I launched FileMaker Pro 12.0v5, opened the same file, and the PDF contents are still visible. You will see that screen shot in the next post.
In case your database file may be damaged, create a new database file and follow what I did. Does this work? If not, then reinstall FileMaker Pro 12.0v4 and try updating again to FileMaker Pro 12.0v5.
Keep me updated with any progress.