I also had a similar problem. I saved an AIAI file, which had a layering mask of a gradient over a photo, as a PDF to print. When I open the PDF with Acrobat Reader it opens okokay, with the layering mask. But when I open the PDF with Chrome or Firefox, it doesn't show the gradient.
I couldn't find the problem within the PDF settings. The way I found to surpass this was to flatten the image with the clipping mask (not the best solution, but now the gradient appears the way it should no matter where I open the PDF file).