What's the history of these files? The first time any file is opened in a newer version and is converted you get a save as dialog to prevent accidentally overwriting the old version. This can sometimes happen after a program update, too, so did you recently update ID?
Another possibility is the use of a custom keyboard shortcuyt set that has remapped Ctrl + S to save As if you are using shortcuts rather than the menu.
I'm not exactly sure if these were originally Quark 6 files that were converted with the Markwarze plugin.
The issue is when another user using the same version of Indesign tries to open these, they have no issues saving? The issue is specific to one user.
It happens when you go to the file menu and click save hence that would rule out the keyboard shortcut.
I have blown away the Indesign prefs but still no joy.
Is this a fully patched version of CS4?
Fully patched on all machines 6.0.6
You mentuioned the possibility that these were conversions from Quark. The first time you hit Save with any conversion you would get the save as dialog, and it isn't clear if the problem aoours at that point, or later, after another user has already done the initial save as.
It's also not unusual for a converion to have some quirkiness in general. I'd try the export to .inx from CS4 and see if it makes a difference: Remove minor corruption by exporting
And if not, try trashing the prefs for that user: Replace Your Preferences