In most cases this behavior is completely normal. Because JPEG images are a compressed image format, there may be some differences in detail when you compare a JPEG file to it's matching RAW file. Also, many cameras offer processing that may change the color balance, saturation, sharpness or other characteristics of JPEG files relative to their matching RAW files. Depending on the degree of in-camera processing applied, the differences may range from subtle to dramatic.
RAW files represent an image exactly as captured by the camera's sensor, and offer the most flexibility for adjustment on your computer. In most cases, it is possible to match the look of a camera-processed JPEG image to a RAW photo using Aperture's adjustments. This gives the advantage of not permanently altering your original images, and allows you to alter or completely remove adjustments at any time. You can create import presets in Aperture to add any adjustments you'd like to your images automatically as you import them. See Aperture 3.x: Applying Effects to Photos During Import for more information.
If you don't want to pre-process your JPEG files, consult your camera's documentation to see how to disable any in-camera processing that may be in effect.