Classic freezes after opening a Microsoft osX app

I'm still running Quark 5 under classic (classic boots on startup and quark is a startup item) and if I then open a Microsoft App in X and click back on Quark all I get is the spinning watch icon. (I think this has only started happening since upgrading to 10.3.9)
If a force quit Quark and restart it it then freezes on startup. Force quiting classic and thus restarting both solves the problem. Subsequently restarting any Microsoft apps doesn't affect freeze classic it only happens on the first run of the program.
I have turned off all Microsoft extensions in classic incase there was a conflict but to no avail. I have also slimmed down classic to the bear minimum for Quark to print and work with Suitcase.
Has anybody experienced this before?
(Machine spec is G41gz 1.25gb ram)

Please be very clear it does not "boots classic into osX…" when you log in, or at any other time and although of course that makes no difference to anything when all is well, at times like this thinking like that can make solutions much harder to find.
OS 9 is an old operating system. OS X is a new operating system. Either of them can boot older Macs, and they behave very, very differently.
Classic is not an operating system and it cannot boot anything. Classic is an "environment" - if you like, an emulator or interpreter - which allows a cut-down version of OS 9 to run on top of X so that newer Macs which can't boot in 9 can still run applications meant for 9.
When you hit problems, that matters for two reasons. Firstly, 9 in Classic behaves very differently to pure, bootable 9 and secondly, since 9 in Classic is running on top of X, all kinds of extra things from X might be contributing to the problem.
Provided you can find the disks, reloading Classic on an X Mac should take a lot less than the 20-odd minutes you might need to re-load pure bootable 9 on an older Mac.
Distiller should not come into the sequence "classic boots on startup and quark is a startup item) and if I then open a Microsoft App in X and click back on Quark all I get is the spinning watch icon…"
If "word always seemed to pause for too long on start up during "optimising the font menu" (or whatever the wording is in the splash box)…" are you saying that behaviour is now different? What, that Word no longer pauses but now immediately freezes, or something?
That would tend to suggests a Word or Office, rather than a System problem.
Either way, if it wa my Mac I'd first disable all the Startup Items in both X and 9, and see what happens when weverything is launched manually, in different sequences.
To disable Classic or pure 9 Startup Items, move the Starup Items folder from inside System Folder onto the Desktop.
To disable X Startup Items - helpfully renamed Login Items as the thinking is different - take them off the list in System Preferences>Accounts>(your account name)>Login Items.
With all those items disabled, Restart and manually launch, say, Word. What happens this time?

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