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My guess is that it's resin showing through at a thin area of acrylic. The acrylic can be stretched too thin in the footwell ( a common area for this to happen) when the mold is pulled and if not heated properly, the result is what you're seeing. Let your dealer know and take pictures to send to the manufacturer and your dealer.
I've seen it happen from the ozone jet. The ozone generator oxidizes the minerals out of solution and deposits them right where it enters the spa. It can usually be cleaned, when the spa is empty, with a solution of dry acid and water (be sure to use gloves) and some scrubbing.
Does anyone know how Chad finally resolved his stain issue? He had rust colored stains in his Jacuzzi...at one point, he thought it was his heater and minerals (among other things). I don't know if he finally got an answer though. :-/
Boni--I am sure Chad will answer later, but I believe that he is convinced it was from metals in his water. He usually uses a metal-gone product when he drains and refills and for some reason, on that fill, he did not use the product. He has since drained and refilled with the metal-gone and, as far as I know, no more brown dots.