I had a similar experience with my D60 when I replaced the membranes a couple of years ago. I used the fresh water pump to flush water thru the high pressure pump for a minute or two, then turned the watermaker pump on at zero pressure with the fresh water pump still running... it took another minute or so and finally the pump started pumping. I switched to sea water, cranked up the pressure and it worked fine. I guess it gets an air lock or something that takes a good bit of water to displace. No problem since.
Kent & Iris