I'm not SURE of this...but I suspect the time differential has to do with the direction you approach (or leave) the island from. That's why Michael, when he left in the boat, was told to follow a specific heading. Similarly, the helicopter was told to follow their inbound heading back out, exactly.
It may be that rocket came in on a different heading, probably very close though, and the difference was enough that it arrived about half an hour later in time than it should have.
That'd explain the gear he was setting up too. Looked kind of like surveying tools. I wouldn't be surprised if he continues to do tests from different angles now, and measure the time distortion. If it's not random, he could establish a pattern perhaps...and create a "map" of the time distortions around the island.