Most of what you described are problems that (I would assume) only come about when you screw around with things. I'm not saying you messed up your Rpgmaker, sometimes stuff like that just happens. The database is really the epitome of a skeleton when you first start a project, just so you can get ideas when making your game. Items are left unchecked just in case you're planning on totally revamping your DB (Which you should do anyway, oh, and check everyone on the first item & copy it to every usable item you're gonna make, to make things easier in the long run), and your dudes are stacked on top of each other in case you want to randomly place them around the battlefield. I dunno about Zach, he's just weird. But getting to your current problem:
If it's an event specific battle, make sure you check the game over box instead of the custom handler one, like this:
If you're not getting game overs from regular encounters, then that's just weird. I'm messing around with mine trying to recreate that, but I've got nothing so far
If you're still having trouble, try checking if you have some messed up common event running (Unlikely) or something wrong in some battle event pages (Also unlikely), and maybe check if you have some anomalous tab under your map folders that lets you set that. Other than that, I'm stumped. Good luck.