Excellent, Francesco, it did the trick!
Just for the sake of other poor souls who are plagued by the same problem, I'll review the process here:
1. Run Software Update (from /Applications/Utilities)
2. Select the Java131and142Release2 update and install it
3. Restart ArchiCAD (although it might even work without a restart).
4. Now, publish pdfs to your heart's content through Publisher.
No more Zero kB files!
Alex Zachopoulos
MacBook Pro 17" 2.4GHz, MacOS X 10.5.6, ArchiCAD 11 & 12, WinXP, Vista (well, not really Vista...)