Hi Lilytippytoes (interesting!),
I'll try to explain your camera's behaviour so you can try to get it to work.
If you imagine first that you didn't have the flashgun on the top (and didn't use the pop-up flash either). When you press the shutter button your camera first meters the scene; this means that it's reading how much light is available and adjusting the settings to try and bring out some brightness.
At the same time, your lens will try to focus by picking out neighboring areas of light and dark and using this contrast to find the right focus. If you're in a dark scene (such as your back garden at night) or taking a picture of something with very little or no contrast (for example, a completely blue sky, very foggy day or a completely monochrome/flat wall) then the lens will 'hunt' back and forth trying to find something to lock on to. Until it finds the focus and locks it wont let you take the photograph, hence the problem you're having and also hence why turning off the autofocus lets you take the photo.
To add the flash into the mix... Often a flashgun/pop-up flash serves not only to help illuminate the actual photograph, but also to help the focus. If you imagine that monochrome (lets say white) wall I mentioned above, there's no contrast or detail to lock on to. Most modern flashguns have a red panel that emits strips of red light that project onto the surface to create contrast for the focus to use (very clever stuff eh?!), then just before the picture is taken the red light turns off.
The other function that some older flashguns (and also pop-up flashes) have is this strobe function where is flashes like a strobe light before the picture is taken. The reason it does this is to light up the scene for the autofocus to lock on.
The red light and the strobe serve slightly different purposes though. The red light creates it's own contrast to lock onto and is the most reliable way to get the focus locked. The strobe function serves only to light up what's already there, so it will help in your back garden, but wouldn't help with that blank white wall as there's still nothing to lock on to, even if it's lit up with a strobe light.
If the above all makes sense (please say if it doesn't!) then this should explain why you're camera isn't doing what you want. It's trying to focus and using the flash's strobe to help, but this still isn't quite providing the contrast required to lock the focus and so you're not able to take the photo.
The 'Busy' message is telling you that it's working hard trying to focus (strobing and hunting!)
Hope that helps.
Dave