One potential issue with your processing sketch is that it writes x, y, x, y, x, y, etc.
The Arduino reads x, y, x, y, etc. If a value gets lost, due to a buffer overflow, for instance, the Arduino will read y, x, y, x, etc.
You should probably have the processing sketch write something like (x y) (x y), etc. The Arduino would read the serial data, looking for a (. Then, data up to the space is x. Then, data up to the ) is y.
That way, there is no ambiguity as to which value is which, and you simply discard any values that don't come in pairs.