That's an odd problem i've never come across, and i'm not sure why it's doing that.
About the map coordinates, i never really delved into the map classes in essentials, so i couldnt say, and as i don't script in essentials anymore i'm afraid i can't help.
Although, i'd suggest looking at the check_event method in Game_Map. That may be able to help you with it
I've been helping Cilerba out with your mouse script, but had a couple of questions. I noticed that the top left corner of the screen always registers as being clicked, as well as whatever coordinate I designate. So if I designated (100,100), that coordinate responds correctly, but a portion at the top left corner will also register as well (about 60x60 pixels in size). Any idea what causes it? Also, I'm unsure of how to check if the mouse is on a particular map coordinate, as opposed to a screen coordinate. That second one sounds like it might be something simple, I just haven't figured it out yet.