I'm having this issue for a project i'm working for. I'll keep you updated if I find anyting usefull to this.
Only DBC got changed so far on this project, so i'm assuming that's what causing it. I've only taken a quick look at it and assumed it was all handled there.
But if you say that the coordinates are correct on your client and the highlight isn't, yeah that makes it pretty weird.
But everything texture wise should be handled in Interface/ as Atraxian mentioned.
Some goes for AIO stuff, every highlight or change requires another texture.
The place should be handled in dbc or maybe the lua/xml that handles the worldmap.