G'Day Z,
This has happened to me on many occassions and is not that uncommon on the east coast. I had it happen once at Cronulla, once at Kurnell, once at Byron Bay and also at Noosa river mouth. The amount of charge it builds up can be extremely high in Voltage, but is generally harmless due to the amperage being weak. Doesn't mean it wont give you quite a boot though!

I have seen a 3 inch long, bright spark from just such occassions that I heard and saw from 40 metres away.

The kite generates static electricity as it flies through air that is heavily charged with positive ions. When we get a heavy build up of positive ions usually hanging lower in the sky (almost always cloudy and threatening to storm), the kite gathers and conducts the electricity to the water through the lines, the bar, through your body, the board and into the water which is negetive or earth.
When you let go of the bar, or jump from the water in a normal jump, the conduit or connection is broken and the charge is allowed to build up in the kite as it cannot get to earth. The voltage builds instantly the connection is broken and builds until you either grab the bar or touchdown from the jump. At this point the charge has reached sufficient voltage to arc from you to the water or you to your bar in your case, in the form of a big spark. This spark would be in the vicinity of many thousands and could be in the order of tens of thousands of volts but only milliamps.
As long as you stay earthed to the water with hands on the bar, you will feel nothing as the current makes its way to earth, it's only when the connection is broken that the spark occurs. It is highly advisable to come in and bring your kite down as it also indicates that there is a strong potential for lightning strike.

I have kept kiting for short periods when these conditions have been about, but it ain't no fun when you cant jump

so best to come in and give it a miss for safetys sake.
Have fun and fly safe,
Darren Marshall
Australian Kiteboarding School