IIRC, the discs are from KWRocketry parts. If correct, this is an issue that has been around for quite awhile, and I don't think there's an easy way (if ANY way) to fix it. I get it too, with many of my ships, although I almost never use KW tanks - mostly just the engines. It seems to me that they don't show up until after the ship has been in space for quite a while - a few weeks or more. I never see them on short missions of a few days or a couple weeks.
I've pretty much learned to ignore it, as it doesn't affect anything other than visually. Sometimes, the discs are directly aft of the engines, but don't affect thrust at all.
Edit: In response to @SpannerMonkey(smce), I've never used any scaling in my ships - everything is stock size. Not saying that it isn't a factor at all, just that it happens even without scaling.
MaxxQ's post in problem with modmanager was marked as the answer