I'm very sorry to say this but you're going to have to remove all the tiles and start over. You will never been able to prevent this from leaking fully.
It may also mean removing and replacing the backing as well.
The critical step you missed was the waterproofing membrane that goes under the tiles and in and over the drain pipe. The tiles don't stop the water at all but are for aesthetics only (and to protect the water proofing). What makes the shower water tight is a sturdy backing covered with a water proofing membrane like liquid flash (one I used) when I did my tile shower. http://www.constructionchemicals.com.au/products/waterproofing-membranes/
But there are many different brands. They are a paint on product and very easy to install.
Don't expect your tiles to be waterproof. At best they are only splash resistant. Water goes right through the grout and can also enter around the side of the tile where the grout is. Porcelain tiles aren't quite as porous as ceramic, but most wall tiles are ceramic because they are a lot lighter. These tiles act like a wick and just draw the water through to the back of them. If you don't fix this you could be in for some serious mould issues down the track.
Unfortunately there is no simple fix to this but to start over. I would not recommend just trying to seal it. It's like covering up rotten wood with paint, it won't last and won't fix the problem long term. Although you've got water resistant plasterboard. It won't last long term. These plasterboards are just designed to repel water to keep it out of the gypsum they are made of, not designed to be constantly wet.
Interesting construction that your builder used water treated plasterboard + chipboard for the construction. 6mm or 1/4 in thick concrete based tile & slate underlay board + waterproofing membrane is all you would have needed. I wouldn't recommend tile on plasterboard at all. Even with the layers that he has. It's not as strong.
Since I know how much work goes into these DIY tile showers I will say this. If you feel overwhelmed, call in an expert. They will have the job done in a week and you'll be able to move on with life. But if you're up for the challenge and want to learn to do it right this time, then dive in and go for it!
It looks like the problem is not just the grout (which fills the gap between tiles) but also may be the tile adhesive is separating from the supporting structure (possibly plasterboard/drywall).
You can remove grout from between tiles using a variety of tools designed for this purpose. Then you can re-apply grout (and sealant if needed)
It seems likely that water has penetrated that structure, it might be best to open it up and assess what damage has been done and how the water got in.
In your case you may need to remove all the tiles, repair the supporting structure and re-tile. It's the only way to get the tiles to align neatly at the corners.
Best Answer
If the liner is good you don't need to go down more, though if you replace with the same size tile it may crack in the same place if there's a (evidently) structural issue there.
I'd be inclined to fill the hole with an "accent stripe" of 1" tile so the crack (when it re-cracks, as seems likely) can follow a grout line rather than crack the face of a tile.