Oh man, I totally get where you're coming from with those plugin issues. I had a similar thing happen with a different audio tool on my computer. It was super frustrating! Every time I opened it, it felt like a game of chance whether it would recognize my plugins or not.
Yeah, this topic is almost 2 years old now and nothing has changed. After I boot into Windows (10) and start MB, FabFilter is never detected the first time. I have to close and re-open MB about 3 times before FabFilter gets recognized. Luckily I only have to reboot my system once in a few weeks so, although it's irritating, it's not a big deal.