I'm not sure what you mean by "plotting". I'm guessing you mean the output from the Publisher. If so, you may have a different pen set defined for the Layout - it might be what is showing. If you detail your output process a bit, we're probably able to give you better help.
I guess the SaveAs PDF you mean is the system's Print dialog. This might not be the answer you want, but Archicad 10 in some way uses the OSX system's PDF creator also when Publishing to PDF. So if you have the same settings the output should be the same. OSX's PDf creator is a lot better in 10.4 than in 10.3. You should upgrade - try to get hold of a copy of Tiger (OSX 10.4) from some reseller before it's completely gone. I realize Leopard might be overkill for your machine.
AC4.1-AC26SWE; MacOS13.5.1; MP5,1+MBP16,1