After a day of PAIN I've finally figured a way of sorting this problem out WITHOUT having to revert back to 10.5.8 (however it is a bit of a pain and requires a version of Quark 7 as well).
First of all, open a Quark 8 file and export as a version 7 project.
Then, In Quark 7, export as a version 6 project.
Open the version 6 project in Quark 7 or 8. The font issue is resolved and your text looks fine again. However, non of your transparencies or drop shadows work! Don't worry about this now. Delete everything that is on the page and save this file (I called mine Quark v6).
Now re-open your original Quark 8 project. Copy everything out and paste it into the document from v6. Hey presto! Everything is back to normal and looks like it should. On certain documents you may have to tweak a bit of tracking here or there, but at least the fonts show and the leading is as it should be. Now save this as a new file and away you go.
If you happen to have an old Quark file that were made on version 6, you can just copy/paste your version 8 stuff into that file (this is how I found out about this).
The pain is that you will have to do this every time you need to access a document from before the upgrade. I would also recommend you use the Quark 6 document for new files as well to avoid any issues when sending artwork to a printer later.
Hopefully Quark will release an update which solves this problem permanently for everyone on Snow Leopard!