There’s an interesting article over on the Macromedia Accessibility blog. They take a look at some popular Flash embed techniques and see how they perform in screen readers. The thing that caught my eye, though, was the performance of the Flash Satay embed method. It looks like if you are using Flash Satay, JAWS won’t read your Flash content.
Unfortunately, they didn’t test FlashObject, but they did test UFO – which works in a very similar way – so I think it’s pretty safe to say that they would behave the same way in a screen reader.