How can I get "distorted" gradient fills to copy & paste properly?

Question

Here's the situation simplified: I create a document and draw a circle and fill it with a circular gradient fill. I then copy and paste that circle into a new document. It looks exactly the same, and importantly, the gradient fill is still editable, so I can change the colours making up the gradient, their positions on the gradient-slider, etc.
However, if I draw the circle in the first document, fill it with a circular gradient fill, and then I "distort" the gradient's shape to an oval shape, using the gradient tool — still keeping the circle itself as a circular shape (only the fill has changed shape) — and I then copy and paste this circle into a document, it does not get copied across properly as a "true" gradient fill.
At first glance, it looks the same. However, viewing the circle in Outline mode shows that the gradient fill has been expanded into 100s and 100s of flat solid coloured objects, each one laid on top of another, getting progressively smaller and smaller, and all masked in the original circle shape.
And of course, as the gradient fill has been expanded, it is no longer "live" and no longer editable, so I now can not edit its colours or positions on the gradient-slider, etc.
So, how can I make it so that Illustrator maintains and keeps the correct gradient fill when copying and pasting between documents? I've tried editing all the settings under Preferences > File Handling & Clipboard, but all without success.
At the moment, to overcome this "bug", I have to separate the two document windows by dragging its tab out of the main Illustrator window, so I now have two floating windows, rather than all windows tabbed in the one environment, and I then have to drag and drop the object from one window to the other. Slightly inconvenient, but it does get the job done.
Strangely enough, dragging and dropping DOES work, whereas copying and pasting does NOT. Weird.
However this slight inconvenience soon adds up when I have to do it many many many times over.
And it gets progressively worse, because dragging and dropping does not allow me to place the object in the position I want it, whereas with copying and pasting, I could ordinarily choose to "Paste In Front" to place my object exactly in the same position between the two documents.
In order to overcome this, I have to drag and drop to get the gradient fill across correctly, and then I have to copy and paste a non-filled duplicate version of the object to get it in precisely the same place, and then I have to use the alignment tools to get the two objects to line up. This = major inconvenience.
And all this becomes even worse when attempting to copy an Illustrator object into Photoshop as a Smart Object, because when I then double-click the Smart Object in Photoshop to edit it, the gradient fill has been expanded — because, obviously, the object had to have been copied and pasted to get it from Illustrator into Photoshop, and this is the problem that Illustrator seems to be having.

Answer 1

Thanks for the continuing answers guys, mucho appreciado.
However, to go through what's been said since my last post...
I tried launching Illustrator in another user account on this machine, but it wouldn't even launch! I got some error number (which I don't recall offhand, but I can re-check it later).
To clarify, this is an official install of CS4 (so no pirating here!), and Illustrator was not running in my other main user account.
And the InDesign thing wouldn't apply to me, as I don't use that app at all. I do invariably have a couple of other CS4 apps running though, usually always Photoshop and Bridge.
I CAN understand how copying and pasting from Illustrator to InDesign would cause this though, because InDesign doesn't support live editable gradients to the same advanced degree that Illustrator does, so it has to expand it when doing so, thereby losing its editability.
Copying and pasting whilst staying completely within Illustrator though is a different story.
You know what — I just had a thought... What if this is nothing to do with Illustrator, but is instead something to do with my Mac OS's system-level clipboard?
I actually had a 3rd-party multiple-item clipboard item installed some time ago, but then never used it. Maybe there's still remnants of that floating around and that's interfering with it somehow?
I'll see if I can clear out all traces of it and see if it makes a difference... Fingers crossed!