Hate to say this but your carpet probably never got fully dried out. The backing is about 2 inch thick foam. The water gets sacked in like a sponge, even a vacuum extraction machine won't fully dry it.
The only solution is to pull the carpet, dry it out fully for about a week inside a warm ventilated space and use the time to find out where the water is coming from.
On my car the foam drip trays around the roof drains were punctured and leaking. I replaced those, the sound deadening under them and sealed the lot with spray rubber seal. It was a ton of work but I now have a dry Boxster.
The design around the rear drains sucks.....
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