Mr. Coffee seems to know the future

Your coffee maker puts water into the grounds at the same rate regardless of how much ground coffee you have put into the filter. The water will stay in the filter area for the same amount of time regardless of the amount of coffee in the filter.

If there is less coffee in the water, then there is less of the flavorful soluble coffeeness (various amino acids, caramelized sugars and aromatic oils) for the water to pick up. The same amount of soluble material becomes more dilute in the greater amount of water. Some coffee makers adjust for this and release less water at a time if you are making a smaller amount of coffee.

If the water sits longer in the grounds of will pick up more flavor, but not all of it is going to improve the flavor. If it sits too long in not enough grounds it will become more acidic and more bitter.

Alton Brown has a great episode about the science of coffee, BTW. http://www.foodnetwork.com/shows/good-eats/2-series/true-brew.html

Your coffeemaker is punishing you for mis-measurement ;-) If possible, measure by weight, instead of volume -- perhaps you can entirely avoid the situation!

There are a number of factors in how drip coffee will extract, including things like how coarsely/finely the coffee has been ground, temperature of water, total extraction time, water drip rate, filter size and type, quantity of ground coffee, freshness of the beans, how soon since roasting, and many other factors. We have several good questions about some of these factors at the drip-brew tag at Coffee.SE. Any of those factors (especially temperature and coarseness of grind) could cause what you reported.

Assuming that the only difference is the quantity of coffee grounds (i.e., all other parameters are kept the same), I see only a few things that could cause what you're seeing:

• More grounds has more total "stuff" to go into the brewed coffee. More grounds generally results in stronger brew, and this will be noticeable from the first drip to the last, if you're looking at the filter output or in a clear carafe or so. (@Marti also noted this in his comment on another answer). You'll certainly see that, cup after cup, the brew will get lighter in a drip brewing session.
• More grounds will take longer for the water to drip through the beans. I think this is perhaps what you're reporting as the "pale first cup" syndrome. For example, the grounds will "stack" higher in a pile, and so the first drips will drip through more beans and more slowly, making it look darker. The grounds themselves will absorb water as the water is dripping over and through the grounds. Coarser grounds will show a (relatively speaking) "weak" brew at first, because the water doesn't penetrate quickly or efficiently into larger chunks of beans. This could be a similar manifestation that you're seeing; less grounds means less water absorbed, so the first water comes through the cone more quickly, and has pulled out relatively less of the "stuff" from the beans.
• If you have a coffeemaker that has a very wide drip head (akin to a shower head), you may be getting some water down the side of the filter that hasn't hit any beans, especially at the beginning. Pouring down the side of the coffee filter is not recommended (better to pour closer to the middle of the pile directly over the grounds), and your auto-drip might accidentally be doing this if you have a shorter pile of grounds.

To test some of these, try to flatten out the pile of grounds (if you don't already) by shaking the cone/basket gently to even out the pile. You're not trying to pack or tamp the grounds in any way, but rather just evening out the pile so that the water can contact it more uniformly. Also check to see that all of your grounds get evenly wet pretty early on in the brewing process; my auto-drip maker is terrible at this, so much that I sometimes end up with nearly-dry grounds at the end of the brew (and weak coffee!) -- bad news all around. You probably don't want to "take a cup out of the carafe" before the entire brew is complete, despite the fact that some auto-drip carafes will let you do steal the carafe while brewing (without the brew going everywhere). Coffee will extract different "stuff" at different times, and you're best to get the whole batch through and mixed uniformly before taking a cut.