Try leaving the opposite direction?
I have a similar problem: all exits are mirrored or rotated, i.e. To reach the map to the right i have to leave to the left, etc...
I tried some of that. If I exit from the bottom of Lion's Way, I can travel to High Hedge, though I arrive at the bottom of the area, not the top as would seem logical. If I then exit north out of High Hedge I can get to Crossroads and then on to the Friendly Arm Inn.
For anybody who's interested. I had a backup of my install from just after installing the BG2 tweaks, so I was easily able to test multiple solutions. I found that installing the Huge worldmap instead of the Large worldmap resulted in all the areas appearing as normal. Other than that change, my install order is indentical to the one I attached earlier.