I have a document created in InDesign from CS5.5. I was trying to export the document with layer enable PDF. But in the output PDF, one of the layer is not coming. I am on Mac OS X 10.6.8. Below screenshots shows the exact problem of mines:
If you test only on the same computer there's a chance that some other software running on that computer is the cause of the problem. By using differnt computers, as you have, the possibility that it's an external conflict is reduced, but not eliminated entirely. I think the next test would be to try it in Safe Mode to be sure there is nothing but the OS and ID active, but the evidence seems to indicate a bug at this point, and that probably means you're out of luck unless you can find a workaround, like putting something marked as printable on the layer as well.