I have had similar problems using Microstation. I am using Microstation version 08.11.07.171.
When creating the 3D PDF file from within Microstation using the print function, go to the 3D plotting settings and deslect "Convert wireframe geometry" and Convert annotations".
Once I deslected those two options, then recreated the 3D PDF files I was able to open them with the data parsing error.
Hopefully this will help for you too.