First cup of the day ony fills half way

I live in a Florida town with ridiculously hard water. There are eight limerock mines within 5 miles of my house for a reason, and I'm used to dealing with the build-up of calcium scale in my appliances.
I started getting the half cups about 6 months after using the Keurig. The PREVENTATIVE cleaning instructions call for running vinegar through the system for 4 cycles. That may be sufficient for regular maintenance, but once you're getting half-cups you're going to have to work a bit harder to dissolve that calcium. Most white vinegars have only 5% acidity (pH 2.4), so you'd actually be better off running pure lemon juice (pH 2.2) through it.
It took me a while to dissolve the crud, but now it's making full cups again.
Here's what I did:
1) Run 15 cups of vinegar through it, pouring the vinegar in the cup back into the reservoir each time 2) Wait 30 minutes 3) Run another 15 cups through it.
What "should" happen (with the largest cup size) is:
1) Run cup #1 2) The pump draws up 1/2 of cup #2 from the reservoir immediately after the cup #1 finishes pouring 2) When cup #2 is started, the pump draws the other 1/2 of cup #2 and starts pouring 3) No water should flow back into the reservoir from the flexible overflow spout during the pouring of cup #2
If this isn't what you're seeing, keep running vinegar the same vinegar back through it. Vinegar will dissolve the calcium, but it takes time.
Hope this helps.

You may be turning the off button of your brewer off too early after your last cup of the day. I noticed that if I don't let it ramble on with the loud noise, as the water is lowering into the chamber after I have a cup of coffee, my next cup is short on water.

Have you cleaned the exit needle? Seem to be clogged up, more info here: http://www.keurig.com/help/B60_Use&Care_guide_spreads.pdf