Not sure where your observations are being made on the hydraulic fluid. Does your tractor have a sight glass for hydraulic fluid or is this all coming off dip stick observations. Unlikely on a new tractor to get any water into hydraulic lines, other than a very minor condensation contribution.
I am thinking your just seeing air foaming of the hydraulic fluid occuring in the hydrostatic case which makes it appear milky. And then after shutoff, the air bubbles leave the hydraulic fluid, resulting in a clear fluid. I see this occuring all the time in automatic transmissions on cars and trucks, where high speed usage foams the fluid with air. Just make sure your hydraulic fluid levels are all at proper levels.