My original post was only regarding the Aegis and Borg Sets, causing flashing.
After this latest patch, every map I goto blinks uncontrollably like someone is flicking the light switch.
It looks horrible and has ruined nearly all immersion as it is completely distracting.

Original post with video:
http://forums.startrekonline.com/showthread.php?t=194405
Comments
I have the same issue and replied in your original thread and I think it is tied to a general bloom problem in STO. It's extremely overdone, and I use a very generic GeForce graphics card and no exotic hardware at all.