Okay I have figured out the fundamental cause of the issue: One of the offset maps on Sevault Canyon was wrong(quest\main.dat instead of quest\town.dat) I have confirmed that making the change will fix this for next version.
In the mean time if you wish to continue playing here are the steps you can take:
1) get to a interior map(i.e. Pokecenter, etc) or a separate member of the sevii islands
2) save and close and reload your game
3) reload game and confirm that map behaviour has returned to normal
4) if you really want to explore Quest Island anyways change your offset map settings to the lowest setting(this will disable them) before leaving the dock or flying into Seven Island Town
This bug is also the cause behind this bug:
https://pokemon3d.net/forum/threads/17970/
and could have caused many other bugs
if you experience a bug on Seven Island please confirm you have followed the steps above and have not re-triggered this bug
If possible confirm the bug else where
