I ran into a similar problem just now. I think I used to (in a previous version) be able to use stored EC to power cyclotrons, but now they seem to have a load % purely based on power generation rate. I solved it by adding a lot (dozen gigantors) more solar panels.
EDIT: No, I was wrong. It wasn't adding solar panels that fixed it, it was actually fixed by spending time while the experiment was running with another vessel focused. It seems that although the cyclotron doesn't want to actually use all my EC for some reason, Retrograde Kuarqs only decay while the station is focused, but still generate while it's unfocused. And once you have 50, they stop decaying.