I had all these problems and also shortened all my wires. In the end I bought another leisure battery, and that worked okay for a short while and then I had the run about again.
Then my flow controller packed up and I have worked ever since without it and I still use my original battery and it easily pumps 1000 litres before I charge it again.
Flow controllers are too temperamental and are over-engineers pieces of rubbish which messes us about, cause stress and cost us money.
Well, that's been my experience of them. There's cheaper and simpler controllers on the market; I'd advise people to go for those.