I seem to be having the same problem. I've placed an .eps file of a simple gradient logo into the document, however when I export to PDF (print), it does one of two things depending on what I choose in the advanced settings:
1. If I choose 'Rasterize: Nothing' from the dropdown menu, I get my clean vector lines but no gradient, and;
2. If I choose to leave the advanced settings as is, I keep the gradient but the logo becomes pixelated because it was rasterized in the export process.
I ensured both times that 'Allow advanced features' was checked. Any other ideas on how I can export this entire file while still keeping the vector gradient?