I have a macbook pro with retina display, and an external monitor attached. Whenever I open a javafx application (and also Scene Builder), the controls inside the window are 'magnified' to about twice the size initially. If I drag the window to my other monitor, and then drag it back then everything is ok.

MacBook Pro (Retina, 15-inch, Late 2013)
2.6 GHz Intel Core i7
16 GB 1600 MHz DDR3
NVIDIA GeForce GT 750M 2048 MB

Thanks.

PS. If theres a known work around I can implement in my code that would be useful to know.