Not too sure what you are doing exactly (short answer: use sort?).
But when you do copyLocations = locations, you don't do a real copy. You copy the reference of locations to copyLocations, so both point to the same array list!
It might be simpler to create a new array list in copyLocations and set() to there. At the end, you can do locations = copyLocations if you want.

sort isn't a option.

note for people who strand here,
the method from the previous post doesn't work in processing 1.5.

I managed to do it with sort now.

Right, I figured that Jquery has the same spirit too, the great trick was on function and variable allocation statement

I have no idea what it was.
I tried to recreate the bug but then it doesn't appear.
strange