This has been an issue in NEI since 1.8, apparently, and I didn't see anything on the issue tracker about it.
Here's what happens when NEI is loaded:
https://www.youtube.com/watch?v=NKcXvl_qSIM
I know the video is old, but it is exactly what is happening to me. I narrowed it down to NEI after reading this thread.
With NEI, flickering, just like in the video. With NEI disabled, there is no flickering. I tested it on 1.11.2, with NEI 2.3.0.223, and Forge 13.20.0.2315.
My loaded mods(minus NEI)

Update: It appears to have started again, without NEI loaded. It took a few minutes, but it did. Sorry to bother you.