I'm not sure I can answer your problem exactly but it looks like you might not understand a couple things about the flight computer so perhaps the following info will help:
Do you understand the startup blink sequences of the LEDs? When you fire up your Phantom and the lights are blinking yellow, it's establishing a GPS lock. When the lights flash rapid green you're ready to fly, and the Phantom has registered it's current position as it's "home point" where it will return to in Failsafe situation.
There are 2 modes for your flight computer, Phantom Mode and Naza Mode the default is Phantom mode.
In Phantom mode, the left toggle switch on the RC basically doesn't do anything. The right toggle has an up and down setting, by default both up and down are "NormalFly" however the down position can be configured to manually trigger Failsafe mode (return to home) or Normal Fly via the Phantom Assistant software on the Basic / RC tab. This is imo a very useful feature, it can be used if you NEED it (like you're far away and lose orientation) or if like me you're just a bit lazy and don't want to manually fly the Phantom home and descend if you're up very high, it can get a little boring descending from 200+m at 2m/s.
Notice I haven't said anything about CL, HL, GPS vs ATTI mode? That's because those features are only enabled if you switch the Phantom to Naza Mode. THEN the right toggle becomes GPS/ATTI and the left toggle can be used for CL and HL. In my humble opinion Naza mode is actually a bit more risky because there's more that can go wrong due to both CL and HL modes change the way the sticks operate.
Honestly, unless you are an expert pilot and want to utilize the advanced features my personal preference and advice is to stick to Phantom mode and trigger Failsafe manually if/when you desire, and let the Phantom do most of the work for you. You should of course test the feature and home lock position at short distances so you can get comfortable that it's working before relying on it at long distance... and don't forget that you can regain control at any time by flipping the switch back up to NormalFly.
I see your post count is only 1 so it's not a crazy assumption that you're a fairly new pilot, I would highly recommend against full Manual mode you should research it more yourself to fully understand how it works but basically it's you flying without any navigation assistance or even auto-hover. way too much work imo.
Now you see why I'm not sure your question "why is GPS not working" is accurate... unless your Phantom never home-locks (rapid green flashing) then it's GPS is working, it's just the switches on your remote aren't doing the features you seem to expect because it's in Phantom mode and there is no ATTI vs GPS mode... Phantom mode is essentially locked to GPS mode.
