PDF export (especially from GDSII) can be a fairly memory intensive process. Please try any of the following:
1. During PDF export, please try using a lower "Plot Resolution (DPI)".
2. You may also want to change the Advanced Option "Smart Detail" to a larger number. This option ignores objects that are less than X number of pixels on the PDF; thus saving data size be eliminating tiny arc segments.
3. For best results, please verify if your machine has at least 2GB memory.
4. Our product Visual Chip is more targeted towards handling GDSII to PDF files, and may better suite your requirements.