Ok although you didn't provide all the info I will need to come out with an exact deduction, I will make some guesses here:
the lighting condition is too low, you were probably taking indoor shots, or evening/night outdoor shots of plaza sing. When you use flash, the camera will be set to think that since there is flash, there is enough light, and it will use a fast shutter speed, say 1/60s, to capture the scene. But your flash range is limited, to say 3m, so large and far subjects like buildings will not be illuminated enough, so they appear dark as the exposure is too fast at 1/60s.
However when you don't use flash, the camera knows there is no assisted light source, so it must take the scene as it is. The scene is dimly-lit, so the camera will use a slower shutter speed, say 1/2s, to capture the scene. And that will be the correct exposure, that's why you said the pic turned out to be what you see with your eyes. However, 1/2s is too slow for humans to handhold, our hands will tend to shake and move. So using a tripod is necessary. Alternatively, you can try to bump up the ISO so that the shutter speed can be faster and thus reducing camera shake, but the noise level will increase. Note that you can only increase ISO in the manual modes and not in full auto.
Hope this explains your encounter.