If it's actually OS9 rather than OSX + Classic, check the Startup Disk in Control Panels and reset to OSX.
Check for some program that causes Classic to start up at:
Control Panels: Accounts
Select his username and go to the Startup Items tab to check them out. There should only be native OSX items there.
While you're there (I think you said you did this so if you did, ignore) go to Control Panels: Classic and uncheck:
Start Classic when you login.
But while you're there, go to the Advanced tab and run:
Rebuild Classic Desktop
And, with Classic running, go to:
Check the box at:
Show Background Applications
... and see what is running. Should give you some clues.
If that doesn't work then:
... and check for Classic items there. If file associations are wrong, it may be using an OS9 version for one of these programs even though an OSX version exists.
You can check that by Control-clicking the app or script and seeing what's under the Open With: field.
You can also check by doing a get info on a highlighted file (Command-I) and checking the Open With field (might need to click the arrow to expand it).
You might want to check the items in that folder against what is listed under Accounts: Startup Items
There might also be a StartupItems folder in /Users/Library. See if that folder exists (might not) and if it does, then do the same there.