Well, you pinned it down to WiFi interfering.
Kind-a odd though ...
I have a very large sketch with a lot of effects on it, which I control over WiFi.
I run that sketch on a ESP8266, just like your Wemos D1, yet not a single effect flickers.
Can you post the bare minimum code with an effect that flickers and WiFi enabled?
My gut tells me that something is triggering an interrupt - just cannot find anything in the code sniplets you have posted before.