I'd give it some more time. My pond has a large, red-dirt watershed, and its water stayed consistently muddy for the first 4 to 5 years, but it now clears within 2 or 3 days after a heavy rain.
I theorize, that after a few years a new pond's basin develops a scum/muck liner. This liner, provided it's not disturbed by livestock or other means, seals the pond's basin and traps the sediment, preventing the re-circulation of the sediment.
As a result, anytime the muck is occasionally stirred up from the bottom it'll quickly settle back down thru the clearer water, as opposed to it becoming suspended in the formerly turbid water.