No, I did not find solution to this problem.
I took the "clean" assembly (added only your mods, nothing more).
Kerbal Space Program - 1.3.0 (version 32 or 64, no matter difference).
Your mods - the latest versions.
Game - new.
I have an vessel (cockpit with a pilot and an engineer of level 5, tank with uranium, reactor without fuel). The reactor is cold. I can not transfer uranium in the reactor.
The same thing happens if the reactor completes its life (for example, about 2 years), and self-extracts its fuel.
I can not transfer uranium or waste.
Below is a link to the cloud, there saving and video. Plus a little translation into Russian, which you did not have (is not completed, literary adjustment is required. I can do this a little later).
https://cloud.mail.ru/public/8rvQ/K4aSsRVuu