I will look into it. What did the generator's GUI say? And how full is the bat box?
The batbox gets freshly placed for test runs, so it will be empty. However I have just done a run with a Medium engine and that behaved as expected (a rate of about 12.5 EU/t before and after the pips). What was new to me this run was that the generator's liquids bar filled up. It hadn't done this with the Small engine, so I would assume the generator can't retain pressure with only a single Small engine.
Still, now that I've got the Medium engine I'll be using that and the Small engine will be relegated to powering the pump for the Medium engine's water.