It seems that the blinking icons are still there. This problem was reported at least two time.

Here some reproducing step from @Danitman:

just switched to Feral to try out. Shred, rip and tiger's fury blink. I'm at the ?? damage raider's training Dummy in DreamWalk. It also does it at the garrison dummy.

Also, I was able to get this problem with the Assassination Rogue on the deadly poison spell.
Yet I don't understand why sometime there isn't any problem, and why sometime, there is this problem…

We need more information to track this bug…

We don't have any blinking problem reported anymore.
We also don't see it anymore.

We will assume that it wasn't a problem on Rotation Builder, but one on Blizzard side which was fixed since.