Problem one - some documents. Certain documents, like the Pages '09 template Word Processing > Reports > Visual Report simply refuses to create any document. You can choose the menu item in the Print dialogue, you can enter a file name, but then you get a message: "Alert Couldn't create PDF/X-3 document."
Problem two - resolution. This limitation was likely here even before Leopard, but it is worth mentioning. PDF/X-3 does not support layers, and that means that the PDF/X-creator has to rasterise vector graphics over pictures, like text over shadows. The problem is that Mac OS X rasterizes to 72 dpi, and that is no way good enough for printing on most modern high resolution printers.
The resolution is defined in a Filter in ColorSync (Applications > Utilities > ColorSync Utility). Go to Filters and check the properties for "Create Generic PDFX-3 Document". The resolution is defined next to the "Flatten Transparency" checkbox. The annoying thing is that the Filter is read only, so we cannot change the resolution.

What we can do, is to create a copy of the original Filter and change the value there. (Do not try to change the values for Trimbox or Bleedbox. I do not know anyone who has made them work.)
Next, is something you should NOT do. The entry in the Print dialogue to print to PDF-X is defined in /Library/PDF Services. Do not be tempted to change any of those entries. You will get a warning message saying: The behavior of this workflow may have changed because of the reasons listed below. The workflow was saved with an older version of the action "Apply Qua... If you try to resave it, you may break it and stand with one less working entry in the Print dialogue.
Instead, to solve the resolution problem, follow the following steps.
Setup
- Open ColorSync.
- Go to Filters.
- Click on the circled triangle next to the filter Create Generic PDFX-3 Document and select the option "Duplicate".
- Double click on the name of the new filter and change the name, if you want to.
- Expand the filter elements and change the resolution to 300 and 300. You do not need to save the changes, but you may want to quit ColorSync and reopen it, to make sure that the change has been taken into account.

Usage
- Open the document you want to make into PDF/X.
- Print to PDF (standard PDF).
- Right click or control click on the created PDF file and select Open With > ColorSync Utility from the pop up menu.
- In the document window in ColorSync select the filter you created above from the list in the bottom left corner of the window.
- Click on Apply. (The Filter list will be reset to "None" through some quirk, but do not let that scare you.)
- Select Save or Save As... from the File menu. You will now have a high resolution PDF/X file. Probably.