Darn - thought I had it with the mac classic thing. I'd suggest that you look to see it the extension is being added to files when they save to their own hard drive. If so, and it's not getting placed on the server, the only thing I can think of is to make sure that Apple menu/System prefs/Network & Internet/Sharing has Windows sharing turned on under services and that Windows file sharing is on under Firewall. I really can't see why this would effect things but it's worth a try. Quark 6X has been noted to have quite a few server related issues, but the most common is corruption rather than extension stripping.
If the local saves (users drive) are not having the extension placed after the file, the user will have to make some changes. With the Office apps, make sure that Append Estension id checked in the Save window. Once checked this stays checked and all docs get ".doc", ".xls" etc. You could check either Preferences or the Save box for Q6.5 to see if that option is present. Photoshop extensions are set in Preferences/File handling. You are given the choice to append extension never, always, or ask. Indesign and illustrator seem to append automaically.
The user can click on a file's icon and then go to File menu (in Finder)/Get Info. You'll see Open With. If you don't see anything else next to Open with click the little triangle. You select the app to use to open the document. Then go right below that to assign that same app to open all documants of that type. I have Photoshop picked for things like .jpg or .tiff and Illustrator picked for .eps etc.
Please note that users can always put an alias to an app in the Dock or on the desktop. To put it in the dock just find the app and drag it to the dock - creating an alias. A document can be opened by just draggin its icon over the appropriate icon in the dock.
One thing you may or may not know about Quark and Indesign (Q equivalent in Creative Suite). You cannot import Q 6 files into ID. You have to Save the Q6 as Q5 then open the thing in Q5 and downsave to 4. It then will open in Indesign. Don't know of any recent fixes for this problem. If you don't have Q5 you could have a problem transferring docs for Q6 to ID.
Using OSX 10.3.8 on a G4