The Bermuda Triangle theory is definitely out there among Lost fans. And we already know there is SOME sort of time warp issue with getting on and off the island (that half-hour gap with Daniel's rocket-thing and then Sayid mentioning to the pilot that they'd taken off at dusk and landed at midday). But how bad is it, and why is it there?
We already know it sucked in a jet plane when Desmond failed to type in the numbers on time, and that it crashed Naomi's helicopter, and that they had to drug Juliette to get her there because the last part of the trip was a "bumpy ride."
The recap episodes are great for some partial clues to this issue. In the last one the narrator (Michael Emerson) said that the EMP that issued when Desmond turned the failsafe key made the island briefly visible to the outside world. This is how and when Penny's searchers in the igloo-type scene "found" the island briefly.
This also tells us that, in general, the island isn't easily found because it's not "visible" to the naked eye.
As for why Desmond was affected on the helicopter, yes, I agree. Remember that in Daniel asked Jack and Juliette point blank: Was Desmond recently exposed to a high dose of radiation or an EMP?
Desmond episodes always are a lot of fun, even if they tend to rely too heavily on the actor's ability to just freak out with amazing skill and believability.