Er, speaking as a fan of Doctor Who and other time travel shows/stories, let me put out a theory on how it could work -

Think of each world as a stream. When you are in the stream, you are carried along by the current (time).

However, if you are OUTSIDE the stream, you can pick which point you enter it at (probably with certain limits or else it becomes an easy cop out when the plot gets too complicated).

The current and movement of one stream has no bearing on the current and movement of another. So, having been carried 300 years downriver in one stream doesn't mean that someone in another stream has gone any distance at all (turgid waters, what can I say?).

This theory assumes time is relatively constant once you're in a stream. That is, you can't easily go back in time in a world you have already entered. You either can't change past events or can't change them easily (since these are the Lost writers, I'm not betting against real time travel - plot altering kind of stuff - coming up, I'm just not worrying about it yet).

Or, if it's easier, think of the fairy tales where someone spends years in on world only to find no time has passed in the realy world - or the other way around. The amount of time passing in FTL doesn't have anything to do with time in our world.

Snow White, for example, had her adventures within about three years of coming to our world - but her story has been told in our world for centuries. Obviously, the times between worlds don't match up.