Can be seen here: https://www.twitch.tv/videos/2181134172?t=6h45m44s on the shaman and warrior in bottom group. Happens every time the debuff is allowed to stay on the target for a longer time.
This is the first time I am having this issue after using similiar settings on other buffs/debuffs. Is it some weird interaction specifically with the Wrack debuff perhaps?

The settings I use for this status:

and use it on the health-colors indicator:

Yeah, the debuff Wrack ticks for more dmg every times it ticks, so I guess something happens for the split second after a tick when it is updating the dmg it does (tooltip changing perhaps?). Because the elapsed time (the text on bottomright corner) remains the same. https://i.imgur.com/DHgXt9g.mp4

I noticed you can also see it on the text-indicator in the bottomright, which has the status Sinestra>Wrack, which is identical to the one above except it turns green <15sec elapsed. And it so happens that the same time the health color flickers, that textindicator turns green for a split second.

That flicker happens when a buff/debuff is refreshed. For example every time the expiration time or number of stacks change. Nothing has been changed in the addon code related to this, It was always working in that way.