Check the Ink Manager in both files to be sure you aren't converting spot to process..
Don't think that's it, the spot colours do not show in the separations preview when the linked file is an indd file, and they do show when the linked file is a pdf.
Did you check? It really sounds like Spots to Process is enabled in the receiving file, but I would expect that to affect PDF as well.
I tested on CS6 and it's working correctly, but I don't have CC on thei smachine, and no time this morning to boot up the other one, so perhaps somebody else will test for you to see if they get the same results.
I decided to try it in a new document, and it was working fine. So I went back to the other document, and checked, and it wasn't enabled. So I enabled and disabled it, and now it's working fine. I still don't know why this morning it was giving me a different result for INDD and PDF, unless I accidentally activated a shortcut.