You may try cleaning with acetone first though. Possibly you didn't get all residue off. The acetone won't harm your marble, but it will clean everything off it.
If that doesn't work, then the ebook. Just a tip, but since you have new marble, you may consider getting the "Cleaning Marble Secrets"... it includes all info in the "etching" ebook plus everything else you need to know about proper marble maintenance.
My freshly installed bathroom has mostly Chocolate marble tiles around the walls and bath.
In the areas where silicone has been used - the water spray the fitter used to enable wiping the excess appears to have washed a contaminant off the wet silicone.
The white crusty marks disappear when wet but return when dry.
They are worst around the bath (horizontal surface) but are present to a lesser extent around all the walls, floor joints and around the sink where silicone was used as well.
I have attached a picture - I have more but could only upload one.
I hope you can help - nobody I have talked to has any experience of this.
Mick, it looks to be etching. 100% silicone won't do this, but something in whatever was used has corroded the marble surface causing the light and probably dull spots.
If it was the spray, you'd see spots from where the spray hit the surface and plain water won't etch marble.
I'd say your installer is going to have to remove all the caulk and restore the damaged marble with a marble polishing powder like ETCH REMOVER / Marble polishing paste designed to repair etching.
I suppose there could also be a reaction between the caulk and any sealer that was applied. Sometimes strange things happen when chemicals collide.
Before removing it all, just remove an easily accessible area and try the Etch Remover. If that works to restore the shine and color, you have your answer.
If not I don't have another answer for and I'd recommend getting a marble restoration pro to take a look. Seeing the problem in person often makes a big difference, but I'm pretty certain it's etching... disappearing when wet is usually a tell-tale sign.
You'll be able to remove or diminish staining at the surface, but the problem is that the source of the stain is still there and most likely will continue to leach through to the surface creating a stain again.
The procedure for cleaning marble stains is cheap and easy to do, so worth a shot.