Your old 600 may have been the loose ball (or caged ball) design and the newer Dura Ace a cartridge bearing type. The loose ball Shimano headsets had a much lower stack height than their cartridge bearing models.

I installed a Shimano 600 (HP-6400) loose ball headset with a stack height of 33mm in a '92 Trek 1420 to replace the OEM Tange headset and it fit fine. When it wore out 15,000 miles later I tried to replace it with a newer Ultegra cartridge bearing headset (HP-6500) but the stack height (37.6 mm) was enough taller that it wouldn't work.