Are they still on their way to the boat and taking longer because of the time issue? or does something happen the the helicopter?

I think it could be a little of both. We know Sayid gets off the island, so one would assume the helicopter makes it to the ship eventually.

Everyone seems to come and leave the island in that storm. They are still flying.
I wonder if they realize how long they have been flying?

I'm guessing that Frank doesn't, or is not able to, follow to coordinates Daniel told him to and they end up back on the island. Nobody looked to happy about that!