when you compare a double-extender with a block on top and one that doesn't have a block, you will notice that it behaves different and the in the D.E. without a block, the bottom piston pushes the top piston, then retracts and pushes again. it looks like a normal 1-tick pulse, but with the BUD it isn't. on the first extension, the movement is instant (abnormal).

http://youtu.be/lVh_F1KJK58
setup is the following:
8x1 tick clock -> 3 tick repeater -> block ->powering the lower pistons and redstone-torch ontop the block to power the top pistons

somewhere in this bug lies the reason for a bug on bukkit (http://youtu.be/IOawoo2l4KM from 0:00 to 0:22)
even though this behaves allmost normal, it is a bug. it should be solved because the bukkit team has the policity not to interfere with vanilla bugs.