The initial question (and topic) mentioned just "Save" so it's a little confusing.
I see your edit about "grayed out items". Save/Save As are always grayed out if you haven't actually changed the document. If you open it, make any change at all, it shouldn't be gray. Is that the case?
Aside that, Save As not working, you should consider the old .zip fix to see if it works for you (although you will need windows on VMWare or perhaps newer versions of some OSX apps support .zip repair):
That may repair your issue.
If not and it's nothing proprietary you can shoot me a PM with a direct download to the FLA and I can see if I can repair or salvage it.
Always keep several backups and never save over a network!
The question is actually very specific and you're terribly wrong.
When using Save As... the location box is sometimes greyed out (I deleted all preferences to fix this) but the problem is that I can't click the "Save" button or anything in the "save location" dialogue sort of box.
The above project was not saved because that's impossible.
Anything in that Save As:, Where: and Format: box is unclickable. I can't cancel, so the project is lost forever. I can't save. I can't change the save location. If I want to keep working I have to keep Flash open indefinitely.
This also applies to any file browsing in Flash Pro CS4. I can't import music to my library, for example.
I meant the File->Save option should not be gray if you "make a change" anywhere in the document. I only have access to an OSX Server remotely to illustrate this point so SimpleText should help you understand what I mean by a grayed out menu item:
The big red arrow.
You can get to the Save As dialog so clearly grayed out menu items wasn't the issue. Moving on..
Your screenshot buttons may be unresponsive but they also aren't "grayed out". Here's a Save dialog with a truely grayed out button:
Your button is not grayed out.
Accurately describing your issue here will help quite a bit. The "save crash" issue has been so rampant it's the first suggestion I had so I offered it. Often repairing the FLA fixed the saving mechanism.
In your case I honestly haven't come across your issue so I have no more suggestions outside reinstall Flash completely. Good luck.
From your screenshots i get the impression that the save as dialog is somehow glitched into the document panel. So while its visible it could be that it has no focus and thus neither keyboard or mouse works on it.
Try to use Window>hidePanels beforw you open the save as dialog and see if that fixes your problem. Under Windows the default shortcut is F4.