When I run the heater I get a purple color on the pool surface

Absolutely not, they are not interchangeable! Each set of wires, go to a specific sensor or switch. The opposite end of that wire goes to an electronic circuit board with specific logic. It is in constant communication and or waiting for communication/confirmation, from that specific switch or sensor, so that a specific action can be taken for a specific situation, all based on that specific sensor or switch that it is connected to. So therefore do not rearrange the wires.
purple wires usually go onto a pressure switch. Red wires will normally go on to the automatic gas shut off switch, or AFS.
there are usually two sets of two wires for the high limits, and they are colored orange. Because there are two high limits.
Brown wire, I'm not sure of? I don't remember any brown wires on a master temp. Is it possible that the brown wire that you see, has discolored and it was an orange wire, or a set of orange wires previously?

Recall of RAYPAK pool and spa heaters

I would assume this is by design. If water were not flowing through the heater it would constantly cycle and mineral deposit would accumulate on the heating elements much faster and shorten their lifespan.

try running the heater with the filter removed or on bypass . preasure (water line)switches are often the guilty party. and in some casses you may need to bleed the gas line to get fresh gas to the unit, you can use soapy water to check, that the fitting leak free, after bleeding at the block

is the heater running ? did u raise the temperature higher that the existing water temperature in pool ? are u running the pool pump long enough to achieve the temperature that you want ? IF CHECK (OK) 1- check the internal flow valve control is located between the cold and hot water little black cap, check the condition ,make sure no calcium deposit build inside, 2-is the water temperature in the heater is the same as the pool temperature ? is the pump got full prime with no air ? is the filter is clean ? is this heater propane or natural gas ?

enough salt? too much salt?
running enough hours per day?
adequate flow to activate salt cell? (cf dirty filter)
Salt cell clogged with calcium deposit?

I run into similar problem. Generally means filter is dirty. Run filter on RINSE or BACKWASH for a few seconds then try again. I am sure this is the cause.

Usually under $100 and easy to replace. Comes with instructions. The tricky part is knowing which wires to connect so make a good diagram of the original to match up with the new in case the wire colors are different.

I just had the same problem resolved, my mastertemp 400 would run up the temp to 82F and then cutoff, the service light flashes and then 50 seconds later the heater would restart and run for 2 minnutesbefore shutting down again and relighting in 50 seconds. Repeating until the temp setting is reached.

I had the pool guy out 3 times until he found a bad thermal regulator valve (kit #77707-0010). Once replaced the heater runs great.

He told me that it's my pool chemestry that is to blame, I had it checked (like I do weekely by me and monthly by the pool supply store) and it perfect??? I'm now questioning what caused the corroson and stop it from coming back?

I hope tis helps.