Hi, I have tried to reproduce the issue using Galv Layer Graphics plugin + KC Mirror Plugin but do not seem to be able to. I have 1) tinted the screen yellow via event command, and then 2) created a new layer. After this, when I enter/exit the main menu, I do not notice any blinking. See gif: 
Viewing post in [CGMZ] Light Effects for RPG Maker MZ comments
Ok, sorry I could not help much, but I need to reproduce the problem first before I can investigate what is happening. You could try some kind of preloader for your water layer graphic or whatever it is that blinks. It could just be that the plugin is struggling to load it in time when it also has to load mirror sprite + light sprites, I am not sure.
