Are you sure it isn't th esupply valve or joint where the showerhead is attached?
Your shower was not built per code...it requires the waterproofing to be sloped so any water that gets to it can drain - when it is flat, any (small) amount that reaches that level sits there and stagnates. This can build up quite a bit.
It could be they did some other things wrong, too, like put nails in the liner over the curb and now the level of water below has reaced them, or they may have blocked the weep holes in the drain, preventing any water that could escape to do so.
You'll get really good info on tiled showers at www.johnbridge.com.
My guess is that you'd have to at least tear out the pan and a foot or so of the walls to install a new one correctly. You may also need to repair the subflooring. If you are lucky, it could be from the valve or supply piping and you can get to it , but it doesn't sound like it.