I don't know edgecam, however, I can't imagine it would be much different then other cams.
It sounds like you may be missing the the island area of the pocket selection. IE Pocket starts here and ends here. Assuming the island is the same Z level.
If the island is at a different Z level then the outer edges, you'd have to set the pocket depth to not remove the island. Again, sounds like your "ending" selection in the pocketing isn't being given.
Just my thoughts.