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The water in the upper chamber of my Berkey system does not drain all the way. Is this normal?

Yes it is normal as this is a gravity filters and there will always be a little water left in upper chamber, and not unusual for the last 1.3 cm. to 2.5 cm. of water to remain in the upper chamber. By design the water must pass through very fine micro pores within the elements in order to pass from the upper chamber to the lower chamber. The lower the water level in the upper chamber, the lower the pressure available to force the water through the micro pores. You may have noticed that the system purifies much faster when full than when half full. That’s because there is more water pressure. The only way to remedy this problem would be to enlarge the pores of the filter elements. This would of course, reduce the efficiency of the Berkey purification system. During each cycle the water left from the previous cycle mixes with the water from the current cycle and is then purified. There is no need to be concerned about the excess water during normal use. Should you however discontinue using your filter for a period of time such as during a vacation, it would be best to empty both chambers before departing and leave them upside down to dry on the dish rack.
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