Hi Chris,
I feel bad considering this update is a result of the thread I started about this issue but unfortunately, the patch actually made it worse. Now the flickering, which was visible some of the time but not in almost every overlapping ship situation, is more present than not.
In case you're wondering:
MacBookPro Retina Edition
I7 Quad-Core 2.7GHz
Nvidia GT650M 1 GB
16 GB RAM
OSX 10.9.5