Hi, fishypete here.
There's a float and a magnetic switch in the fill tube; it's probably blocked by a bit of debris or a root and keeping the switch from accurately indicating a low water condition, producing the constant blinking.
The pump issue could be a few things.
1. the pump may be failing. It's a small magnetic drive pump, and the impeller (the small shaft with a rotating plastic blade inside the motor) may have worn out. Usually you can tell if you have a motor that requires a few taps on it to get it running.
2. the electrical contacts that connect at the back of the bowl and the lamp arm might be dirty, or not connecting properly. Jostling the unit may be getting it to connect.
3. certain models cycle the pump and it might be in the off position. I assume you've noticed it going on and off if you have that model, so I'm assuming this is not the problem.
4. the pump will eventually fail and need replacing. If this one is 3 years old that may be the problem. Properly cleaning the impeller regularly will keep it working the longest, but these types of pumps have a limited lifespan because the run nearly constantly and heat and wear attack the epoxy encapsulated motor, the shaft/impeller, and the walls of the impeller well.
Hope this helps,
fishypete
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