Pic 2

Pic 3

That tile is very pretty.

I thought that sealing the grout was to help prevent staining, not to render waterproof.

Do you know what waterproofing system, if any, was used behind the tiles?

@Linelle - IM not saying sealing would make it waterproof, but from the pictures you can see how the lower tile grout is stained and dark compared to the rest of the tile grout

@jerzeegirl.- I know they used a vapor barrier, but honestly I'm not sure what kind.

Well, from looking at your pictures, there are at least 3 possible causes of this discoloation on the tiles.
The first one, though remote, is that they used a different color grout instead of the light grout they were suppose to use. I highly doubt it, they usually mix enough up at one time and do the whole tile job at once.
The second one, is that moisture is getting down behind the tiles and that is mold showing through.
The third is they used a cheap horrible grout on the job, and the shower may have to be regrouted.
Did you use a good grout cleaner with bleach just on the dark tiles yet?
Do you notice any odor at all?
If you are not satisfied with the action that the builder takes, I would call a professional for his opinion, and see what he thinks.
The builder, might not be totally honest with you, he might just want to run a warranty out.

#2 is what I'm concerned of. They used one bag of grout throughout, and it is a quality product so I don't think it's those. We've used dial soap and scrubbed often cleaning once a week (recommended vs other cleaners by local tile store). We'll have to give the grout cleaner/bleach a try.

If it's moisture getting down there, then scrubbing won't help. Grout is porous and won't t totally prevent moisture from getting through. This is why it's important to make sure the waterproofing behind the tiles is done properly. You should find out from your contractor what was used behind the tiles. Is the black grout on the bottom of all the shower walls?

This post was edited by jerzeegirl on Sun, Nov 9, 14 at 12:07

Yes, it's dark all around the bottom row of tiles being darkest right up against the shower pan. Looking closer, it actually looks like there is some mold underneath the clear caulking along where the grout and pan meet. It's darkest on the wall where the shower head is, almost as dark on the adjacent wall, and the shower seat across from the shower head wall is slightly lighter.

Does look like black mold. Take your pictures over to john bridge tile forum.

There was another poster with dark areas that looked like a moisture problem but turned out to be product scum typical cleaners didn't budge. A cleaner was recommended and worked. Search for azmom.

It looks like moisture to me. From the photo it looks as if the tiles are darker too (not just the grout). John Bridge is a good idea.

We had something similar happen. The grout didn't darken on the bottom row, but the tiles did. We used a different shower for a few weeks til it all dried out, then re-caulked the base.

In our case, the bottom row of tiles were cut and were exposing a more porous surface right at the area where the caulk is. When the caulk ages and starts to need replacing, the moisture seems to wick up and the tiles get darker. I guess it's one way to tell when we need to re-caulk...