The problem with synchronization may occur with following glass calls:

setMaximize
setMinimize
setBounds

As X server / Window Manager response is asynchronous and it's impossible to directly wait for the request to finish.
This may lead to some of the race conditions below:

1) Application execution continues, while the response arrives after some code was executed. This response is then treated by Scenegraph as an "event" (e.g. setBounds changes the bounds, then Scenegraph changes the bounds again, than a response arrives changing the scenegraph bounds to the previous state).

2) Different events arrive (leading to an execution of Java code) before the response arrives. Unfortunately, there's no way to wait for the response without processing events that arrived earlier.
This is generally not as big issue as 1), as it usually doesn't cause any problems and events are actually processed in-order.