I see that you have a Minimoto Electric Go Kart from the parts that you have purchased from us.
That type of problem where the power cuts out and then cuts in again when the throttle is released and then re-engaged points towards the either the batteries or the controller as most likely being the problem. Most controllers do not have overload or overheat circuits and will not cause that type of problem so chances are pretty good that it is one of the new batteries. It could also be the circuit breaker however the breaker is least likely of all the parts to cause that type of behavior.
The only way to know for certain which part is causing the problem is is to perform a load test on the battery pack. This test could be performed with a multimeter by reading the Voltage of the battery pack while the go kart is being driven to see if it drops under 33 Volts right before the power cuts out. The battery pack should be at around 41 Volts when fully charged and should only drop around 1 Volt when under load.
Before performing the load test I would individually test the Voltage of all three batteries to see if they all have equal Voltages to begin with. Each battery in the pack should have around 13.8 Volts when fully charged. If one of the batteries has a significantly lower Voltage reading than the rest of the batteries then that is bound to be the faulty one. The batteries can be individually Volt tested without removing the wires from them as the wiring harness does not interfere with the Voltage test. It is a good idea to have the go kart's power switch on when Volt testing the batteries so they have a small load on them.
Hopefully the problem is simply a faulty battery which you can get replaced under warranty. If the batteries pass the Voltage test and also pass the load test then the next thing I would do is temporarily bypass the circuit breaker with a jumper wire that has two 1/4" spade connectors crimped on each end and see if that solves the problem. If bypassing the circuit breaker does not help then at this point you know that the batteries and circuit breaker are good and can presume that the controller is most likely causing the problem.
Please let us know if you have any questions, and if you do not have any questions then please let us know how it goes.