Map Layers issues

One of the last remanding issues to figure out with my hack has to do with a new section I've opened up in Thamasa. Those who've played the hack are probably familiar with it - it's the area in the upper left that you go to to get to the new Esper Village place. Well, the fence tiles there have a problem where they show the character's head poking through for a second. I have copied the exact same tiles as another fence I used as a reference, behind Strago's house. I can't for the ****ing life of me figure out why my newly opened up area's fence won't behave like the other in terms of layers or whatever dictates how the character shows up on it, NPC layer priority I guess it would be.

Like I say, I've copied both layer 1 and 2 tiles for the Strago's fence the exact same, so it should behave in the same way I'd think... but it's not. Here's a horrible quality vid just to show what I'm talking about. I first show Strago's fence that works, then go down to a fence I made just purely for testing/showing, it's a carbon copy of Strago's fence, both layers. Then I go up to my opened up area to show the issue there:
https://youtu.be/ij9CZXRD97w

Also, I have issues with other opened up areas such as this graveyard, with the bush tile:
https://youtu.be/RI3RyqFYsa0

The bush tile does the same exact thing, as well as those gravestones, which is why I put those dark green solid can't walk on tiles in front of them, and then sold it off as a fresh-looking grave. Again, I copied the same exact tiles that the WoR Mobliz uses for it's gravestones, and other bushes in maps where this issue does not happen.

SO, it seems anything that's not already on the original/non-modified map has this issue going on... which can present a huge problem I'd imaging making new custom maps... My question is why, and what can be done. Why doesn't my exactly the same property tile fence act the same as Strago's fence!?!? I've even tried as a desperation attempt to put invisible NPC over the fence tiles, but sadly that did not work as expected.

Here's another visual aid to show I know what I'm doing in terms of re-creating the same fence properties:
http://imgur.com/a/5FSp7

Also, while I'm at it, in LE, selecting the bush tile or flowers tile also in the tileset always has caused a error/crash of sorts. I've always wondered about why it does that as well.