I talked to Kilgore on IRC about this earlier.
It seems there is a low-level encounter protection feature that is either bugged, not fully finished, or on it's own program and not playing nice.
He indicated that it would be fixed once the scripter who has been working with the Worldmap scripts is able to work on it.
Other than that, no other information was given. I also didn't ask.
NOTE: The above is a representation of my personal recollection only, and should not be taken as 100% accurate or factual.