As OOG wrote after your comment, it's the Macs with 10.4 that are creating the duplicate files! I had the same problem with my system. Using a SBS 2003 server to share files, at first it was Leopard that was creating duplicates - I fixed this (somehow) and now Leopard works great (even with Quark 6.5) but it's Tiger 10.4 that is now creating duplicate files.
A duplicate file is created as soon as you double click to open it - adding 'copy' to the filename and then 'copy 1', 'copy 2' etc every time it's opened.
So, I open the server volume called SHARED and click on a file called TEST, I'll see a file called 'TEST copy' appear on the server and a dialog box says copying 'TEST' to SHARED and Quark will open the file called TEST copy. Do it again and I'll have a file called 'TEST copy 1'
This only happens with Quark files not Word nor InDesign nor Text.