I've reproduced it on ubuntu 13. We, seems, got this trouble initially on ubuntu 13, I don't know about other platforms.

Run that strange app several times and don't touch anything. Wait 2 seconds.

Output is different. It could be this :

Button@5d8d7f6a[styleClass=button]'stage1'
BoundingBox [minX:301.0, minY:128.0, minZ:0.0, width:63.0, height:26.0, depth:0.0, maxX:364.0, maxY:154.0, maxZ:0.0]
Button@427dff52[styleClass=button]'stage2'
BoundingBox [minX:301.0, minY:156.0, minZ:0.0, width:63.0, height:26.0, depth:0.0, maxX:364.0, maxY:182.0, maxZ:0.0]

Or this

Button@5d8d7f6a[styleClass=button]'stage1'
BoundingBox [minX:301.0, minY:128.0, minZ:0.0, width:63.0, height:26.0, depth:0.0, maxX:364.0, maxY:154.0, maxZ:0.0]
Button@427dff52[styleClass=button]'stage2'
BoundingBox [minX:300.0, minY:128.0, minZ:0.0, width:63.0, height:26.0, depth:0.0, maxX:363.0, maxY:154.0, maxZ:0.0]

You should look at minY of button on stage2.

Depending on run, it could be 128 or 156. That is bad. Because our robot clicks in different position.

you can click the button to get new output. I have specially aligned buttons to have them placed at the same coords.