I came across this bug aswell while testing the new reactors in sandbox mode. It might be related to the Quantum Vacuum Upgrade as the unupgraded plasma thrusters in my career save still work just fine. Another thing I noticed is that, while Antimatter Collection, Fuel Reprocessing and Tritium Breeding all seem to now work without the need to timewarp or have the vessel active (which is great, thanks Fractal!), the decay of Tritium into Helium-3 still only works under very high timewarp for me. On a craft with about 4000 Tritium on it the decay only showed at 10000x speed and higher.