Double-clicking - OS 9 apps launch, but documents don't open

On my G4 dual 450MHz PowerMac with OS 10.4.3 and Classic...when I double-click on a Microsoft Word 2001 document or a Quark 5 document (an document created by a classic app) the program that created the file starts up - like Word or Quark, but the window for the document does not show up.
So in the application I have to go to File->Open to open my Word docs or Quark docs.
Also, I have the Quark 5 and Word 2001 icons in my doc. Strangly, if I drag my Quark & Word documents on to their respective dock icons, the programs start up, but still the document's don't open in a window.
When booting in OS 9, double-clicking on Word & Quark documents opens up the app and the document.
I tried rebuilding the OS 9 desktop from System Preferences.Also rebuilt the desktop using TechTool. Ran DiskWarrior on the hard drive. Cleaned out a bunch of caches with Onyx. I used DiskUtility to 'repair permissions'
Any suggestions?

I do think the docs are meant to open from double-clicking and in all seriousness, I think there's just at least one layer too much going on for the Mac to keep track and the poor user can't get round that.
My Mac has never remembered to open the XPress documents I double-clicked, even though it launches Classic 9 and XPress.
If double-click still fails to open a doc when its application is already running that's a different matter…

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