Hi,
Got a new spa cover the other day, the water in my spa had been clear and within chemical limits. Then it rained the other night and now my spa water is exceptionally cloudy, been working it with the PMS stuff and we will see, could some sorta chemicals have leached off the new top in the rainfall?

Anything is possible... however, you might want to drain and refill to start a new baseline, just to see if the situation continues.