I do have a weird answer for it which is rarely talked about today but it's quite important now when people aren't using CRTs to the same extent.
This is something that just not could happened to the PCE, you would not see this if you were using a CRT, yes if you could it would probably be a badly constructed power supply (or a fridge in the same outlet), anyhow you are using a Framemeister, and what it does is converting the analog signal it to digital, lets say that with other words, it's a digital interpretation of an analog signal, so what you see might actually not be what's actually there, this goes deep down in the calculations of the algorithms of how the scaling and processing is down, the blacks is especially known for this on the PCE on the Framemeister.
That's usually fixed with the Brightness control on the Framemeister, which sounds awkward since it does not seem to effect Brightness, the XRGB-3 had Blackness (黒レベル, Black level) and looks like this function so it might be a mistranslation somewhere, it's set at 27 as standard and 21 usually looks good, I don't know if this would effect the dark blue you're seeing but it effects the the same kind of disturbance you see in that but in black.
The best way to describe the misinterpretation problem is on the GBS-8200 playing SNES with Magical Quest, when mickey jumps the ground he stands on bounce with him a few pixels and compresses when he hits the ground again, it's obviously not happening in reality it's just Mickey that jumps... there's also like a gloria around him when walking that bends and distort the leafs surrounding him, not as obvious thou...