I too did something similar recently. It appears, dithering only works within a sequence independently. Also, its frequency must be set to no more than a half of the sequence length it it won't run at all. I ended up with a repeated sequence of 6 shots: RGBRGB and dithering set at every 3 frames. Effectively it dithers every 6 frames in the middle of each sequence.
The more I use Ekos the more I feel like, for my use scenarios, repetitions should be handled at sequence level, not in scheduler.

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