I would use the initial reading that you are receiving, since letting it sit around, the CO2 might be gassed off (either through the hole where the titrator is placed or elsewhere). It might be okay if it's sitting for a few minutes, but an hour is a bit too long (how long does it take the solution to change color?).
I'm also assuming that when you say changing color, you're referring to the solution going from blue-green to purple, correct?
Phosphate concentration at your level isn't something to be alarmed about. It's only really a problem when nutrient concentrations/levels are out of wack and you're dealing with chronic bouts of algae.