Can you check to see if the water is cloudy directly from the well (before any filter equipment)? Sometimes the backwash timer gets off on my iron filter and it backwashes during a time that I might use water at the house. You could get cloudy water if you use any water during any equipment backwashing. Otherwise, if the water gets cloudy during/after a rain you could be getting surface water down the well (bad).
** Not a pro **