blossom1:In fact it has converted all 6.5 files to 8 whether I have opened them or not, I can see that from their new icons.
I know what you are talking about, but that's not really true. The OS knows that they are Quark files, and because you have Quark 8 installed, it uses the Quark 8 icon to display the files in the finder, but they are still Quark 6.5 files until you open them in 8 and save over the 6.5 files. The reason that I point this out is that you can still open them in 6.5 if you want to, which you couldn't do if they had been saved in 8.
You could try making a new Quark 8 doc the same size as a 6.5 doc and appending the layout (that's similar to thumbnail dragging, so you may get the same results, but its worth a try).
There have also been some issues with Suitcase Fusion, so you could try searching the forum for some tips on that. I'd also try clearing out your font caches. And keep in mind that if you have used system fonts in the Quark file like Times or Helvetica, the system fonts on the new computer may not allow you to activate the other copies, which could be different (I couldn't say from here whether that's true or not, but possible).