Did you put the HV transformer directly on a reactor chamber? I do and i get the bug aswell maybe it has something to do with the HVT im going to do some tests now.
EDIT:
It has something to do with the energy net, if you activate your reactor and leave the region/chunk so that the reactor is out of the player chunk loading range the reactor stops producing eu. To start it again you have to break a wire and replace it. The HVT has nothing to do with it happens with and without one regardless of the placement inside the energy net.