I highly recommend using PHD2 for guiding. I had problems like you are describing for at least a year, up until early July, which is when I switched to PHD2. Since then, guiding has been much much better.
PHD2 is fairly well integrated with EKOS, but it does require that you start it up separately from kstars/EKOS. This has not been a problem for me.
A very useful part of PHD2 is Guiding Assistant. I highly recommend using it for 2x or 3x your worm period before you start guiding.
Anyway, I don't mean to diss the guiding in EKOS, but it seems that implementing a guiding algorithm is a lot harder than it might seem at first. PHD2 has so much good stuff in it, plus excellent documentation. I don't know what the magic is, but I'd give PHD2 a try.