Could be "Detail Tiles" also. Things like small plants growing on top of tree stumps will cause the tree stump to become passable.
Heres how it all works:
If a Tile is not marked as Priority (the ones with the Star that go over the Player) then it checks Passable on Layer 3, then 2, then 1. So for the tree stump example, layer 1 would be grass, layer 2 is the stump, and layer 3 is the "detail". If Layer 3 is "not empty" (the tile in the top right corner), not a Priority (has the Star 1, Star 2, etc), and IS passable, the engine uses Layer 3 to determine if the player can walk. The problem here is in each tileset, there are a LOT of blank (but not "empty") graphics that can all have passability settings, so finding these is usually a nightmere.
Dont worry, there is a TRICK!
In the editor, on the spots you are having problems preventing the player from walking, RIGHT CLICK, dont left click, RIGHT CLICK on that Tile on Layer 3. Right Clicking will cause the editor to highlight the Tile that is in use in the Tile Pallete to your left. Thus, it should have a White Box around it. If you have a large tileset, it is much more difficult to find. And there is another solution to this. After you've right clicked on Layer 3, left click on the Scroll Bar to make the Tile Pallete window active. Then press the down key on your keyboard once, then the Up key on your keyboard once. The tile that is in use there should now be both highlighted with a White Box and it should be displaying, even with really big tilesets.
RIGHT CLICK works as a COPY
The Right Click to Copy works to highlight which tile you are using, but only if you Right Click on ONE TILE. You can Right Click and highlight multiple Tiles at the same time, but when you do this, it wont show which tile is selected. To "Paste", just Left Click on your Map on the appropriate layer. When you "Copy" also, Autotiles do their Auto thing. But guess what, there are even more tricks you probably dont know about.
This is unrelated to the issue with your map however, its just a point of info. If you hold down SHIFT while drawing an Autotile, it completely fills in that Autotile as if it were in the Center. If you use another tile to draw over an existing Autotile, it will NOT AFFECT the Autotiles on your map. This allows you to do things like put Grass on top of Water or Water on top of other types of terrain. There is a Water Autotile that has only Water, but none of the Terrain that is below it. So you can put water on top of Stone, Beach, Cliff, Grass, Dark Grass or ANY other type of tile.
Back to the Glitch
There are many scripts that alter Passability. If your issue is not caused by some sort of Tile, then it may be caused by a Script. You can fully disable a Script without deleting it by putting "__END__" at the very top of the script on its own line, no quotes. Do NOT put ANYTHING else after __END__, even SPACES.
__END__
This will prevent anything in the script from running. I recommend the top line because you can easily check that it is "disabled". Deleting scripts that require settings are a nightmare to go back and reconfigure.
Downloading your map now, but its large so I'll just make another post once its done. By broadband barely qualifies as high speed. Damn rural interwebz...
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Edit: I cant find it. There is no DATA.
If it is an issue, duplicate your entire project so you have a backup and delete anything that is not relevant and still has the bug for us to find, then upload that...
