Yes, Afterglow works by taking pixels which would otherwise be black and if they had color on previous frames this is blended in. If the pixel’s color was never black then it will never get any afterglow. It was something like this that I had run into, so I had to move the color correction affecting the black after the afterglow pass.
In the end I switched to the mame phosphor persistence method which doesn’t have this issue. It also only requires 2 texture samples rather than 5-6 samples.