Hi, as TSR_MapOverlay is a paid plugin it will be difficult for me to troubleshoot the conflict. Before I contact the author and see if there is anything that can be done, could you try changing the order of the plugins in the Plugin Manager and seeing if that solves anything?
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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.