Aquatrol power

Does the timer control both the pump and the SWG? If the timer turns them both on together but then the pump turns off while the SWG is still on you could risk damaging your SWG unless you have a flow switch that will disable the SWG. As to the pump, if it turns off and on when it should only be on it sounds like it's overheating. If this is an above ground pool your pump may have reached the end of it's life.
 
Correct. I unplugged it for that reason. It just started doing it yesterday or today. The pump is two years old. If I take the pump plug out when the controller has it off, and plug it in directly, it comes on just fine . That’s why I thought it was the timer or transformer
 
If I take the pump plug out when the controller has it off, and plug it in directly, it comes on just fine . That’s why I thought it was the timer or transformer
I take this the pump works just fine if plugged directly into a GFCI or 120VAC wall outlet.
Manually move the in-house timer switch to the ON position and the controller switch to Auto. If the "Generating" LED turns on and off along with the pump, the analog timer might be acting up.

Disconnect the timer J1 connector from the mainboard to rule out the in-house timer. Install a temporary jumper wire between pins 5 and 6 (see below pic). Power on the controller, move the switch to Auto and observe if the Pump and the Generating LED are turning on and off intermittently. If it doesn't, replace the in-house timer.

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However, if the "Generating" LED stays solid but the pump runs intermittently, inspect the 15A AC socket at the bottom of the panel and the wiring connections. Also, the K3 relay must be checked for cold solder or burned circuit trace.
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