It's OK if the heatsink is electrically connected to ground, this is happening via the screw/nut, and the metal part of TO-220 package positive voltage regulators are connected to the middle (common) pin, which should be at ground.
The capacitor footprints have two pads/holes for each lead. As you already observed, they're connected, so it doesn't matter if the unused hole is filled with solder. The extra pads/holes are so either 50mil and 100mil lead spacing capacitors can be fitted.
As for the voltage problem, I am a bit puzzled... voltage regulators really shouldn't be outputting more voltage than their rating. They can output less, if the input voltage isn't high enough, but more? WTF? :D I'm guessing here, but one way it might appear to be higher is if you're measuring using the black probe on something "lower" than the common pin of the voltage regultator... i.e. I think if you stick a resistor between a voltage regulator common pin and ground, the output will be higher than its rating relative to ground.
Can you test the voltages directly between the middle pin and each of the other two pins of the voltage regulators? i.e. the input and output voltages directly at the voltage regulator pins. Maybe this will be different to your other measurements.