Did you lock exposure (or use manual exposure) to ensure the same exposure between each shot? If not you can get variations from one shot to the next, because the camera's meter can change its mind about optimal exposure as the composotion changes. Also make sure you're not using auto white balance.
Your shots may still be useable though. Many of the commercial pano stitching applications available can blend the shots as long as the difference in exposure is not too great (they also have other capabilities that go beyond Automerge).
I have experience with two applications:
Autopano Pro and
PTGUI. Autopano Pro works well on some panos and does a pretty good job of blending exposure differences, but the stitching is completely autmatic so if it doesn't get it right there's no way for you to overrride. PTGUI is a bit more flexibile, you can align the images yourself using "control points" to get a more seamless stitch on difficult images. It can also blend exposure differences, and seems to be a bit faster than Autopano Pro.
Both applications have demos, might want to give one of them a try and see how it does with your pano.