Water heater pilot lights but burner doesn't ignite
If I understand correctly, your pilot flame is lighting correctly. But the main burner won't turn on because the electronics in the Gas Control Valve don't acknowledge the pilot is lit.

There are two likely faults:


Thermopile is not sensing the flame correctly, or 
Circuit Board in the Gas Control Valve is defective.


To test for case 1, use a multimeter to measure the Thermopile output. It should be at least 350mV. Here are instructions on how to do that:

http://waterheatertimer.org/pdf/Test-thermocouple-and-thermopile.pdf

If the Thermopile output is less than 350mV, you may remove it from the burner and clean off any corrosion.

If the Thermopile output is adequate, the fault lies within the Gas Control Valve. Unfortunately, there are no user-serviceable parts in there, so you would need to replace that entire assembly.