I never faced this problem before,
MB has a lot of problems before 2.5.3 update, as crashing CC 2014,
But it gives you this flickering problem when using any effect,
I just tried it on my windows computer and there is nothing wrong with it,
Windows 8.1, NVIDIA 4000 Quadro,
As I can understand it’s not a hardware failure since the problem came only caused when you render the project, so you can do several things, and I hope it works for you.
Clean PP media cache database
Check sequence setting as it should be matching your footage at least field settings. (Frame options and select non flicker if that isn’t the default option)
Try to use different effects, choose one of accelerated effects or a regular one, and try to see any difference between them
Try to apply these effects on several footage of different codecs as well.
Uninstall QuickTime, reboot your device, install it again and try.
If you have k-lite codecs installed just uninstall it.
Apply these effects on native codecs.
Try to render it using different codecs.
Turning GPU off could be helpful
This could sort this problem to understand what it stands for.