The pulsing light mean you receive at least one sat providing the time data.
Sometimes if you are inside the house you cannot receive satellites.
Go outside just to be sure you can receive correctly satellites, if you are using the cheap chinese 11$ 'OP GPS', antenna is really small and performance is not the best. This cheap 'OP GPS' also do smoke, due to a regulator only allowing 5.5v max voltage input.
Cheap 'OP GPS' ^^
If you want to try the FlexiPort, be sure the changes done in hardware page are effective.
Disconnect all the power (battery and USB) and power again the FC.